My son has condensate building up in his flue and running down into the furnace. It is a 2 stage furnace. The contractor who installed it blames it on the chimney. Is that likely?

Did you have a city permit for the work? Did you have a written contract with the contractor? If the answers are no, you will most likely have to just get another contractor to install a proper flue. If you had a permit and written contract, call the contractor and tell them their work was incorrect and they will need to install the proper flue size. If they say no. You can always file a small claims court against them to pay for the fix.

There are several questions that need to be answered about what type of system you have, but i found this posting that may help:
As your gas furnace runs, is there water leaking at the base? Is the furnace's air filter wet, too?There are a few things that could be happening here. But if you have a high-efficiency furnace, here's the most common cause: a condensation leak.
We'll explain why a furnace creates condensation, and what's causing it to leak out of your furnace.
Note: You'll know if you have a high-efficiency furnace if:

• The yellow energy guide tag says your furnace's efficiency is 90% or higher AFUE.
• The vent/flue pipe is white PVC as opposed to metal.

Why a high-efficiency furnace creates condensation
How in the heck does a high efficiency furnace create condensation/water anyway?
It's all about how the furnace extracts heat from combustion gases.
A lower-efficiency furnace extracts some heat from combustion gases and then quickly vents them out the flue pipe.
But a high-efficiency furnace, to extract more heat, has 2 heat exchangers. These allow the furnace to extract heat from the gases for a longer period of time. This causes the combustion gases to cool and then condense.
That condensation then exits out your home through a drain. But if that water is pooling around the furnace, there's a problem preventing it from draining properly.
Causes of a condensation leak around a high-efficiency furnace

• Clogged condensation tubing
• Clogged condensation drain
• Breaks in the condensation line
• Issues with the condensate pump (if you have one)

You'll need a furnace technician to diagnose which of these is the issue and then fix it.
Other causes of leaking water around a furnace
If you have a conventional, standard-efficiency furnace...then its flue pipe may be incorrectly sized.
If you have a whole-house humidifier connected to the furnace...there may be an issue which is causing the humidifier to leak into your furnace. Your humidifier should be getting annual maintenance from a professional to prevent this.

First, check the drainline from the furnace. You have a 90% gas fired furnace. Where 80% furnace has 1 heat exchanger, yours has 2 heat exchangers. And the second heat exchanger will cool the exhaust enough, that it ends up below the dew point, and your furnace outlet/exhaust will condensate. This drain is probably stopped up. Now, I've installed and service many of these systems and I've only seen the piping at the roof you described once. And that was when the roofers replaced the roof, damaged the furnace flue pipe, and tried to repair it themselves. Normally, and this may not apply to yours, we tie in the exhaust/supply lines about 2-3 ft. above the furnace. Then 1 pipe goes through the roof. Thus 1 pipe is a kit that has an inner liner & outer pipe(2 pipes in 1). Now I'm not sure if this is a problem or normal for your system, but it may be worth looking into. You should be able to find it in the installation manual, or call a local parts house that sells your brand, or as your tech. And if it's just your drain, forget all about the piping I mentioned. Hope this helps!

CHECK FLUE FOR OBSTUCTIONS AS WELL AS COMBUSTION AIR INTAKE FIRST. THEN CHECK TO SEE IF THE FURNACE DRAIN IS OPEN AND NOT CLOGGED [ONLY IF YOUR FURNACE IS A CONDENSATING HIGH EFFICIENCY MODEL, typically the flue pipe will be 2 or 3 inch pvc pipe] over the years more often than not, it is an obstruction or poor drainage which will not prove the pressure switch to allow the burner to ignite. in rare cases the furnace control board could be bad as well.TRY DISCONNECTING FLUE AND COMB. AIR AT FURNACE JUST TO SEE IF FURNACE WILL IGNITE. HOPE THIS HELPS!!!!!!

generally speaking a sealed combustion system is inherently more safe than a system that draws it's combustion air from it's ambient location. however, it cannot be considered 100% safe in a potentially hazardous location. The actual system that would be used in a "code compliant" installation would be a 100% outside air unit.
That being said, you can install this in a garage, the vent that you are referring to (if it is a standard mobile home system) is generally directly above the unit and usually no longer than about five feet. It also requires a listed and labeled termination "cap" If you install 90 degree angles or extend the vent too far you will have issues with condensation in the piping that will cause the pipe/ heat exchanger to fail prematurely.
If the system is a 90+ efficeint unit then the PVC venting is generally allowed to be about 30 feet long, with a 1/4 inch per foot pitch back to the unit for condensation, also the general mfg. instructions allow either 2- 90 degree or 4 45 degree fittings in the line. hope this helps

Gerge, if you go to website www.energycodes.gov
you can do a heat load calc yourself. Basically, you figure out the sizes of walls, total area of glass. total doors to outside, ceiling area and types of building materials used. It is pretty easy and then you will know for sure. The contractor should be suppling you with one but if not use this, it is free!

actually if you vent your furnace by code, it would probably be cheaper to have a chimney liner installed up the old masonry chimney. you may be able to buy a kit and do this yourself. any time a new furnace with a draft inducer on it is installed, it must be vented into the proper flu material. if it was vented into your chimney, it may not have be installed by code for your area. you may talk to the instaled if they are still available and maybe that can return and do it correctly. if you leave this vented into your masonry chimney, the acid content of the exhaust will ruin the chimney. a liner will also get rid of the water problem you have.

That is a fairly large difference. It is usually ok to have the inside evap. coil and blower up to 1 ton larger than the outside condenser. That will make the unit slightly more efficient as well as less likely to freeze up on low airflow situations. It is not recommended to install a new condenser on an old evap coil. There has been a lot of changes to the design of the coils in the last little while. For example a 10 year old 2 ton coil may only have 3 cubic feet of volume but a new 2 ton coil may have 4 cubit feet of volume.

There are many factors that may have infulenced the decision on what size condenser to install. Many of which can only be done by visiting the home and doing alot of work, checking the duct sizing bioth supply and return, inspecting the insulation and windows of the home etc. etc. Most of the time that never gets done. You can blame the contractor for not doing a complete check, but at the same time you can blame the customer because many contractors that are that good loose the job to a cheaper bid that did not no any of the research. It is a catch 22 for everyone involved.

There is ALOT more to sizing equipment that many people think, sadly that also includes many HVAC contractors. Way too many people use "rule of thumbs" or flat out "guess".

Sorry for the rant but your queston can only be answered by a good well educated HVAC contractor visiting your home. That type of a contractor is getting hard to find these days in such a price competetive world.

Most likely either a bad board or no gas to gas valve. Bleed out all air in the gas line. Check for 24 volts at both gas valve and circuit board terminals leading to gas valve. No voltage = bad board.