I strongly vote for another mechanic. His take that a problem EGR also leads to stalling is a new one on me. A plugged EGR is one of the major reasons the 3.5s burn a lot of oil. He thinks it might be a bad transmission (based on sucking noises under the hood???)sounds like code for lets make the poor guy buy a new AT as we have no idea what the problem is. Not saying the shop is for sure bad just that they don't sound like they know beans about Isuzus. In any event a second or third opinion is always a good idea for that amount of money.

Before spending any major amount of money on the AT also get a through check of the engine. No sense in dropping some big coin on a new AT just to have the engine crash.

As to your original shifting problem, that is likely the IMG problem or it could be the very common mode switch problem (search for the details).

As to driving around for weeks with CELs and not doing anything, that is a potential recipe for disaster. If that is how you routinely treat your vehicles then indeed a Trooper is not for you. Sell it now and move on.

What is the story on the proposed AT. A simple salvage pull? A rebuild if so what do they check/do? What kind of warranty? What kind of warranty will your shop give you? Or will they point at the AT place and they point at the shop?

Bottome line - it could be as simple as new IMGs, cleaning the EGR and tubing, and maybe the AT mode switch. Or you could have a bad AT and an engine about to follow suit. While you cannot rule out the latter you can get another mechanics opinion. Hopefully one with more Isuzu experience to try and make a proper decision with all the information.