I would definitely start by re-pinning any of those rough connectors you mentioned, that one on the mpu is looking pretty bad. I know you're looking for a more systematic approach here, but i just see so many problems on these games wind up simply being connectors that needed to be replaced/reflowed.

Ultimately it sounds like your a 5v is probably dropping too low, causing resets/lockups. If the previous mpu board had battery corrosion, it may have creeped into some of the female connectors that plug into the mpu. How is the 5v at the mpu?

Here's the crimper i use. Totally basic, does a perfect job though...just takes a little practice to get the hang of it. https://www.greatplainselectronics.com/proddetail.asp?prod=1028-CT

I've since gotten a ratcheting crimper, but haven't had a chance to really put it to the test. They're pretty cheap and a lot of people seem to like them. One big advantage is that it does both crimps simultaneously. Another case where there's a learning curve to using the tool effectively, but shouldn't be too hard to get the hang of it. Search Amazon and eBay, I've seen these exact same crimpers with over a dozen different brand names. Not sure if one brand is any better than the others, but you can probably find them cheaper if you hunt around a bit. http://www.amazon.com/Crimping-Tool-Insulated-Electrical-Connectors/dp/B07GFLWKTT/ref=mp_s_a_1_2

As far as wire strippers, i have all 3 kinds you showed. The basic pair are perfect for working in tight spaces. I use these for my work tools and home tools: https://www.amazon.com/WGGE-Professional-crimping-Multi-Tool-Multi-Function/dp/B073YG65N2/ref=mp_s_a_1_4

The Capri pair that has a slot for each gauge is a nice design, I'm very happy with mine (though they're labeled Klein). Definitely helps a lot when doing a lot of connectors. Here's the set i use: https://www.amazon.com/Stripper-Electrical-Klein-Tools-11063W/dp/B00BC39YFQ/ref=mp_s_a_1_5

The last one that automatically strips is a neat design but has to be calibrated to the wire size you're stripping (or at least the cheap pair i have is like that). Once set to the correct size, it works very well. Here's a link to the type i have: https://www.amazon.com/WGGE-WG-014-Self-Adjusting-Insulation-Stripper/dp/B071CKX2MT/ref=mp_s_a_1_22

They all work fine. I always keep my basic manual pair handy when using the auto strippers though, sometimes you just gotta get in there and do it yourself.