PTO switch being bad... Uncommon, but probably an easy and logical place to look.
The gear shift lever. Maybe there is a design issue. He is blessed to have a dealer that would send him parts to do a warranty repair on his own. That's not common, for this reason, HE INSTALLED THE LEVER INCORRECTLY. Then he blames it on a yet unknown mechanical issue. My guess is, he indexed the lever incorrectly. He indexed it to neutral, the neutral switch then indicated neutral, but it was actually in LOW. Simple process of indexing the lever correctly I'd presume, which the dealer would have done, if they weren't so kind as to send him the parts to install himself incorrectly.
I'm sorry you are making payments on a tractor that was broken... But guess what, some people pay cash and have $30k in that broken unit, not a measly down payment. Cry me a river. New tractor owner indeed.