Were manual calculation done? It is pretty typical for the upstairs to be hotter, heat rises. I once saw a guy put a 5 and 2 on a two story home. The small unit cooled the master bedroom and it never shut off in the summer. We ended up remodeling a new home to put doors at the top of the stairs to solve the problem. Home owner did not want to cut the exterior walls.
The unit comes on
T-stats are usually located under the return air.
Second the coolant line running from the compressor is 68
Not following the manufacture instructions is always a good way to void the warranty.
Also the vapor line had
Workmanship is a sore point for a lot of people. What is acceptable for one is not for another. Covering the outlet is a code violation.
Were there permits pulled? Has there been an inspection? If you have not paid them do not until they make everything right.
I have seen some pretty ugly air handler runs. But never one with as many
90's as you describe. Smells of inexperence or lack of knowlege.