I have or had several 22RE's that I put a header on. The 86 4Runner had auto trans. The 86 Xtra Cab, 87, 88, 91 and 93 were all manual trans.
In my personal experience, it wasn't the header. It was the diameter of the rest of the exhaust tube. I had good performance with 2 1/4" tube and just generic "Turbo" mufflers from Summit. Anything larger absolutely killed the low end torque. Especially with the auto trans. 2" tube with the auto trans would have probably been better. Never tried it. I always had CAT's in place to pass emissions. Universal ones from Summit whenever I replaced failing stock ones.
Sticking to stock tire size was also important. When I went to 31's it was also gutless until I swapped gears to 4.56's.
All my engines were stock except the 88 after rebuild. It had larger valves, porting, more compression and a cam for more mid range. Ran a 2 1/2" exhaust, universal CAT and turbo muffler because I don't like loud in my old age. My best running 22RE.