What do you suggest?

I'm in a similar position with the shifting, except no rebuild, still original trans (I believe) and 91 octane. I tried playing with the shift time with little success. It's my daily and I don't want to have to do a rebuild if I don't need to. 220k miles...
Although, when I do give it everything ...

The only aftermarket items I'm aware of are the ones I installed. Cold air intake, exhaust, new plugs and wires. No aftermarket stereo, subs, hell, the back speakers don't even work...
I don't mess with anything while tuning.
There was a brake box at one point...I'll try to see if there's a fuse for ...

I currently have the 91 tune installed and I love it. Everything except the shift into second gear. When I'm hard on the gas it shifts perfectly. If I'm just daily driving it, the majority of the time, it's a super hard shift that's very uncomfortable, especially when I have kids in the vehicle ...