On page 25 of the installation manual it states "CAUTION! A separate drain line must be run to the drain from thecondensate trap. DO NOT connect the condensate trap drain into the drain line from the evaporator coil." I would also verify the slope on the line exiting your trap.
What size is this furnace? Even on the 90k up to 24' of 2" pipe is allowed with 10 elbows. Why did they go up to 3"? (See chart on pg 16 of install manual).
As far as thermostat, unless you have a non-communicating heat pump the best thermostat to use with the system is the iComfort.
Definitely check for the wire nut or anything else that may be in the trap.
Each elbow is equal to 5'. So you are saying that the 90,000 can vent up to a total (one one leg) of 74'?