The 2nd shop has been doing a lot better for you than shop #1. If you want to be polite, you can thank shop #1 for his time, but as Mooseman said - do not let that guy near your truck, or any other vehicle you have. He's looked at it personally, and for him to tell you what he told you, in polite terms...he is either dishonest, or inept as a mechanic.
Lastly I’m so confident in our diagnosis that If it did not fix your issue I will not charge you for the repair.
For $1000 (which is way too much to replace either a TCM or PCM, and you don't even have a separate TCM in an '02) - you can put a *lot* of new stuff in a trans (and since he supposedly knows how transmissions work, he could probably completely rebuild it to factory spec for that cost). If he replaced the trans outright (for $2800), then of course it's going to 'work' when he's done. So take that with a grain of salt. Also, as I write this, I think that he sees you're not good with the $2800 for a new trans, so he's trying to reel you in with the $1000 repair, saying that he'll at least get it back on the road for you for that price.
The bad thing for you is that you're not experienced with automotive repair. And for what it would cost in tools & learning time (unless you're interested in learning, which counts for a lot) - you're better off either finding a good, honest mechanic, or enlisting someone you know (friend, significant other, etc.) to help you with this (and it's only fair to compensate them in some fashion.
Stuff like normal 'maintenance' (changing fluids, filters, etc.) is easy enough that you can learn that quickly, with minimum $ investment in tools, etc. And you'll learn more about how your vehicle works (and others that you may have in the future.)
As for (most) of the members here...I'll admit that many of us work on our vehicles because we think dealership costs are insane (and sometimes they don't fix the vehicles properly), and some of us even have the mindset that the only way we'll 'know' our vehicles are fixed - is to do the work ourselves. Generally, we'll save a lot of cash by doing it ourselves, too (and in some cases, the owner can't afford to pay a 'pro' to do it, but they have some mechanical knowledge, time, and money enough to purchase the parts.)
How you benefit from that is to see what we post here collectively...you can see what 'works', and what doesn't...alternatives to save time / effort / money when possible, etc. And as the old saying goes...it's cheaper to keep a good running vehicle, than it is to purchase a new one (although new ones are nice, have a warranty, latest safety features, more fuel efficient, etc.)
To answer your question about changing out fluid & filter... of course, you can do that, and it's probably time for it. And while I don't think it will 'likely' fix your issue...you won't be doing any harm, and might do it some help. Since the trans operates normally now, by performing a fluid / filter change, you'll be extending its life. Actually, assuming the issue is electrical, you won't be 'wasting' time / money on changing the fluid, either - even if it has to be drained to perform the 'real' fix. I won't lie - it's a fairly messy job, especially if there's no drain plug in the pan. But it is something that you could even do yourself, if you don't mind dealing with the mess.