On the intake side, take a look at the pipe going bebtween the air box and throttle body. On my '89 Runner, I was bit surprised to see it actually shrank down to liek 2" or so before expanding again, the tube had a sepereate hose for the smog pump line which got in the way. I think this was only certain year, though.
IMO the only way you will get any real change on the intake saide is to really open the AFM and passage; best way to do that is get an early 80s Supra intake w/ the 3" inlet. If you get the righ year (82-82?) the pinout on the AFM cable is teh same, just plug it in. Now you can run 3" hoset he whole way in.
However, this will help only if the exhaust is also opened a tad. conventional advice seems to be that teh 4-1 styles put the power more in the higher RPMs, while tri-Y is lower end.
I have the Supra AFM mentioned above w/ LCE header, 2.25" all the way, Cherry Bomb muffler and CatDaddy freeflow cat. My power is decent, BUT it seems to really kick in around 3,000+ RPM, which is higher than your average street drving, at least w/ an auto transmssion like I have. I regeared to 5.29 and now it's *great*.