The 4.10's were fine in my daily driver. I drove it to Florida with 4.10's and still got 21 mpg. 3000 rpm at 80 mph is typical for a V6 powered SUV, and that's about what you get with 4.10's in a mark.
If you have a LONG commute, more than about 30-40 miles each way, i'd say you should consider less than 4.10's, but with my 20 mile commute, 4.10's were perfect. And I took the car up to about 140 on the highway with them. Only difference was the car got there faster.
If you like high speed, track down an MMC driveshaft. You need it with gears.
For the converter, higher stall is better WITH very aggressive lock-up. 3500 stall would be fine (I had 3200). But you DO want the converter to lock up under WOT. You also want it to stay locked unless you're stopping or launching. I loved the way my car drove after Jerry originally tuned it - very aggressive lock-up, felt like a manual. Only fault was it occasionally wouldn't unlock fast enough on a stop and the engine would stall. But I did like having the ability to cruise around at 25 mph or less and have it actually lock.
I had a PI converter back in the day, but I hear Lonnie has the good **** now. Give him a call.
For the shift kit - i'd skip it and go with the modifications Jerry outlined. That info should still be on the TCCOA site. All Ford part numbers and just a few holes to drill. It IS a shift kit, but no worry about quality of aftermarket parts, or lack of R&D. I'd rather go with Ford stuff recommended by someone who knows his ****, than with something some tranny guy recommends based on "it shifts harder" with no engineering knowledge. Some of the shift kits will recommend some changes that are very bad ideas - read the J-mod stuff even if you do plan on an aftermarket shift kit, so you know at least some of what NOT to do when you install the shift kit.
I don't know what year your car or your trans is, but if it's a '98 I wouldn't even bother with a shift kit. Even with the other years, 90% of the shifting is based on programming. But if it's not a '98, get in there and do the accumulators and "while you're at it" do the j-mod.