Have a comfort maker Furnace that is about 10 years old. About 1 month ago I notice a "clicking noise": while it ran. The guy cam out and said the clicking was the smart valve assembly and needed to be replaced, while replacing it he noted that there was some water in the base of the blower motor. I was told this was a design issue and that they would replace it with a kit that allows for some water to drain out of a tube that was not able to drain properly. Does this sound correct? We have the guy coming out tomorrow to make the changes to the air output pvc pipe.

Your coils are dirty and until you have them pulled and pressure washed you are going to have a lot of problems. You should also clean the blower wheel. 1/16" of dirt in the cups of the blades kills 30% of the efficiency. I am sure it is filthy and for him to not clean it first indicates that he is a very poor technician. DrTom4444