The flow is more than it used to be when the Rinnai was working fine with two faucets flowing probably triple the advertised flow rate now. It still cycles hot and cold every few minutes. Is build-up a problem? Is $180 a typical cost to clean the build-up out? How often is this maintenance cost expected to be needed? Thank you.

The hot side of the faucet is most likely plugged with something that came up thru the water system. The average thankless waterheater requires at least 1/2 to 3/4 gpm flow rate for the unit to sense flow and turn on. If there is not enough flow it will not fire and heat the water. Not sure about this particular unit but a few require at least one full gallon per minute flow. So chances are that if you fix the faucet, you fix the hot water issue at the same time

The first thing that you should do is get a water sample and have it tested for TUBIDITY. Then see what the contaminates are. This will tell you what the problem is. I seriously doubt what Rinnai is telling you is the truth. Then you need to look into a whole house water filter that has an NSF recommendation. That will stop all the issues that you are having.

1) Guesses: Sounds like a bad single-handled faucet cartridge, or low water flow at faucet, or clogged water filter.
Replace faucet cartridge, clean the aerator, and/or clean sediment out of pipes below sink, and clean water filter at tankless unit each month.

2) For exact measure of problem:
Typical faucet can have 2 gallon per minute flow rate.
2 gpm flow rate means faucet fills 1 gallon container in 30 seconds. Test faucet using 1 gallon container and a cooking timer to get flow rate.
Clean aerator to improve flow rate. Compare kitchen flow rate with other faucets in home.
http://waterheatertimer.org/Low-hot-water-pressure.html

Most homes have 1/2" diameter pipe running to kitchen faucet.
100 feet of 1/2" diameter pipe holds 1.2 gallons of water. This assumes no sediment build-up inside pipes.
http://waterheatertimer.org/Water-heater-recirculation-system.html

Assuming only hot is turned on: If faucet is 100 feet away from water heater, and pipe diameter is unobstructed 1/2" diameter, and faucet has 2 gallon per minute water flow, then hot water should arrive in 36 seconds.
50 feet away, and hot water should arrive in 18 seconds.

If kitchen has single handled faucet, and the handle is raised in the middle, then equal amounts of hot and cold water are drawn at same time. This doubles amount of time for hot water to arrive.

If single handle faucet has a bad cartridge, then faucet can have crossover.
Crossover means that cold water can enter the faucet even if faucet is turned to hot.
Bad single-handled faucet cartridge can delay or stop the arrival of hot water.
http://waterheatertimer.org/Crossover.html

Tankless require maintenance including cleaning combustion parts yearly, de-lime heat exchanger frequently, and clean water filter each month.
http://waterheatertimer.org/pdf/Tankless-maintenance.pdf
http://waterheatertimer.org/pdf/Bosch_Overcoming_fluctuating_temps.pdf
http://waterheatertimer.org/Troubleshoot-Rheem-Tankless-water-heater.html

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http://waterheatertimer.org/Troubleshoot-Bosch-Tankless-water-heater.html#flow
1) Tankless require minimum flow rate before burner will activate.
2) Sounds like the water pressure drops quickly when faucet turns on. This implies combination of problems including sediment build up inside lines, crossover at single-handled faucet, or sediment filter clogged or water softener clogged.
3) Low flow faucets can reduce needed flow rate.
4) Other problems can contribute: sensor failure, loose wires, PC board failure, high temperature setting, cold incoming water temperature during winter months.

Grundfos RCP-96 has Flow range: 0 - 27.5 U.S. GPM
According to Amazon spec sheet:
http://www.amazon.com/Grundfos-RCP-96-UP515-55SFC-Recirculator-Timer/dp/B00128BJAO

Most tankless require .4 GPM to start burner and .25 GPM to maintain burner
Rinnai does not show C85e-1 so you will have to consult your manual to see minimum water flow requirement.
http://www.rinnai.us/tankless-water-heater/
Sample manual from Rainnai mentions 'minimum flow rate' several times but doesn't give specific number. Yet promotion blurb on page 1 says "Ultra operates at a lower minimum flow rate."
http://www.rinnai.us/documentation/downloads/U290-665x0200_Condensing_Manual_EN_FR_1-2010.pdf
Another rinnai manual mentions flow rate several times in troubleshoot section yet fails to define what that rate is:
http://www.rinnai.us/documentation/downloads/U287-1833_VB_Series_R75LSi_R94LSi_R98LSi_Manual_EN_FR_EN_FR.pdf

It might seem that tankless promoters are CTA by failing to mention specific flow rate numbers.
I think tankless promotion is a definite overachiever, and vague flow rate is one tiny example.
It proves the necessity of reading whole manual and asking questions before buying a tankless.
There's another factor to consider:
All performance numbers are based on new products in ideal circumstance, and not based on a 4 year old product located in your home.

Your flow rate may vary, especially over time, and especially if water in your area is not crystal clear, and you are not diligent with correct water softener and filter.
Many factors can affect flow rates: water pressure, number of elbows, clogs in the line, sediment, size of pipe, aireators, water-saving shower heads, local water conservation policies, water well pressure, MUD district pressure issues, your home located near end of a water main, etc.

Read tankless efficiency vrs water softener
http://waterheatertimer.org/Battelle_Final_Report.pdf
Image of tankless parts vrs tank parts
http://waterheatertimer.org/images/Compare-water-heater-parts.jpg
Bradford White tankless vrs tank side by side
Lime scale does not flush out of tankless
Tankless must have water conditions with less than 11 grains hardness
"Savings falls far short of a payback," 'without comparing service costs'
http://www.pmengineer.com/Articles/Cover_Story/8cf9e86f7c298010VgnVCM100000f932a8c0____
Sediment clogs tankless pressure sensor without softener.

clean filter on the cold side coming in and clean or replace the aerator at the sink, rinnai works on water flow, common problem if your water hardness to high or if you have iron in your water

Flow meters can get jammed by silt or debrise. The only way that I know to check this problem it to remove & inspect the part and that takes alot of training if you have a Rinnai (not recommended for the beginner).

One thing you could check is the inlet screen. Turn off the water and power to the unit and drain down. The screen in the black plastic circle on the inlet fitting under the unit. Unscrew this and check how much grit it has collected. Clean off, replace, turn water back on, open a hot faucet to get the air out then turn the power back on. This sometimes improves the flow enough to solve the problem.

I wonder if you have this problem below caused by a drop in water pressure from someone flushing a toilet or a washing machine. I would call the company to remedy this issue.

17. What is a cold water sandwich effect? The term “cold water sandwich effect” is a term that is used to describe the introduction of cold water into the hot water supply line during frequent on/off operation of an instantaneous water heater. The cold water sandwich effect, when present, appears as a momentary drop in hot water temperature as it is discharged from a hot water supply outlet (i.e. shower, tub, or faucet). This phenomenon is present in the operation of all instantaneous, tankless style, water heaters, but is minimized with the high tech design of Rinnai water heaters.
The technology built into the Rinnai water heaters is designed to minimize the cold water sandwich effect. Rinnai water heaters are microprocessor controlled and when water flow through them ceases, they remain in a “ready to fire state” for approximately 1 minute. If water flow through a Rinnai water heater begins within the first minute following water flow stoppage, the water heater will fire back up within 1 to 2 seconds. This minimizes the cold water sandwich effect that would otherwise be experienced with a low tech tankless water heater. It should be noted that the cold water sandwich effect cannot be removed completely from tankless style water heaters. The safety standards developed to insure the safe operation of water heaters require a delay in the ignition sequence of all gas water heaters.
While the cold water sandwich effect cannot be completely eliminated from standard plumbing systems, it can be eliminated from plumbing systems that have a supply and return hot water circulating system. Rinnai has developed 2 methods to eliminate the cold water sandwich effect in residential hot water circulating systems.
The first (and preferred) method to remove the cold water sandwich from circulating systems utilizes a small electric tank water heater (powered up) that is used with a dual purpose. The small water heater acts as a mixing tank to eliminate the cold water sandwich effect from the Rinnai water heater and it uses its electric heating element to offset the heat losses from the hot water circulating system.
The second method to remove the cold water sandwich from circulating systems utilizes a small 2 to 6 gallon storage tank installed on the hot water outlet of the Rinnai water heater. This tank acts as a mixing tank to blend the cold water sandwich with hot water and eliminating its effect at fixtures.

thats because the rinnai does not have a set up for a circulating pump it would make the unit run all the time,, they are not designed to work that way,, you will have to just wait for the hot water to get to the faucet just like before,,don't let any one tell you there is a way once the water flows it turn on the tankless so it would never shut off, you could get on that goes on a timer on say the farthest fauset away from the unit and set the timer to come on like 2 min before you are ready to use the water in that bathroom in the morning or at night other then that there is nothing else you can do

Its A Possibility The Left Over Water In The Hot Is Frozen. If Your Line Is Exposed Outside Somewhere It Can Easily Freeze Up. Turn On The Hot Water Everywhere In The House And If Accessible Check The Lines To See Where The Warmth Ends. You Can Leave One Off Over Night In Hopes That It Will Eventually Defrost.