I have an air handler with this model number and am trying to figure out what size this is in tons??

Usually the 36 in the model number means 3 tons or 36,000 BTU

Will this unit work with a 3.5 ton amana condenser? Does the .5ton on the outside affect the cooling or humidity level of the home?

Will this unit work with a 3.5 ton amana condenser? Does the .5ton on the outside affect the cooling or humidity level of the home?

It might work but the rule books says NO. The inside unit can be bigger than the outside BUT the outside cannot be bigger than the inside. A real pro might be able to adjust down the outside unit BUT here again with utilitys being what they are you will be better off matching the outside to the inside.

Making something work does not mean it will work for a long time or that it will work properly and that is the problem.