Engine runs rough

you have addressed most of the things that cause these codes

https://www.google.com/search?q=2006+Ford+Mustang+P0106+and+P2195


MAP Sensor (as opposed to MAF)
P0106 Manifold Absolute Pressure/Barometric Pressure Circuit Range/Performance O2 Sensor P2195 O2 Sensor Signal Stuck Lean When the O2 sensor reports lean, it is dumping extra fuel which causes carbon fouling. This takes a while to burn off or you can use an 'Extreme Clean' type fuel system cleaner.

https://www.cjponyparts.com/resources/mustang-dtc-codes

..

https://www.obd-codes.com/p0340

A great many wiring/circuit/sensor faults are temperature-sensitive so it is not a surprise.

Jasmina, for VW code P0106 is the Manifold Absolute Pressurer Sensor(MAP) sensor and can cause the issues you described.
i will post links for you to check out and compare.
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P0106 MAP Barometric Pressure Circuit Range Performance Problem

https://www.google.ca/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&cad=rja&uact=8&ved=0ahUKEwjN86bvx_rKAhULuIMKHWtYDpsQFgghMAE&url=http%3A%2F%2Fforums.vwvortex.com%2Fshowthread.php%3F5437331-Persistent-P0106-looking-for-some-diagnostic-help&usg=AFQjCNFw95Y4fLI5tjisHCbOIeLjfDMnag

check engine code P0106 VW Jetta SE 2 5L engine should this be dealer cost

P0106 Code VW GTI MKVI Forum VW Golf Forum VW Golf MKVI Forum VW GTI Forum...

He needs to check the fuel flow as well as pressure , All so a blocked muffler can have this affect

yea that's a electronic problem its probably a sensor

Try Maf sensor,(Mass air flow)
Then try tps sensor, (throttle position sensor)
Unable to answer exactly without looking up codes

some fault codes stored in your car,
use autocom cdp pro cars check your car and clear the fault codes.

P0171 trouble code and a rough idle
Confirm on the P0171=Lean. This would suggest not enough fuel for the amount of air applied. If you air intake wasn't closed off correctly, you may have been sucking excess air and fixing the cover would have righted this if so. It would be possible that your unfiltered air intake may have fouled either a plug or an injector (or multiples). Cleaning plugs is an easy DIY. If its the injectors, I'd take it in. The sensor is probably correct based on your description. If it's throwing the P0171 code then it is sensing lean mixture and the car running rough would support that result.
Not enough gas is the same as too much air in the air-gas mix.. There could be a vacuum leak downstream of the mass air flow sensor. Vaporize some kind of carburator or throttle body cleaner (not in excess when hot keep face and hands at a distance)around the intake conduits and hoses while the engine is running. When the engine idle changes, you will have found the position of the leak.
check all vacuum hoses foe amsplit or tear.

click on the below links for code details.
P0106

P0121

P0171

P0174

P0335

P0340

P0385

P0442

P0506

P0507

P0601.

all of the above codes seem to have a common cause, they all list a bad ecm (computer) as being a cause, and the last code P0601 points specifically to a bad computer. sorry for the bad news, hope this helps.

Remove the housing that covers the engine block and look behind the engine block, up against the firewall towards the bottom of the block there are some vaccum hoses(this is easier to get too if the car is up in the air, or lifted on jack stands) get yourself a aerosall can of brake cleaner and lightly spay around all the hoses til you find your leak( the vehicle must be running) be very careful cause the fluid you spray can catch fire if it hits the exhaust manifold when it gets hot. good luck