ok..... gonna fix some things here.... AGAIN.
4afe's (at least the earlier engines) use a smaller crank, with a 40mm rod journal size.
one of the better setups you can do (and i HAD this posted on vvt-i until a mod took it down... i guess i put it in the wrong place

) in my opinion for a fairly reliable 4age setup would be:
early 4afe block (7 rib)
early 4age crank (pre 87)... all 4age cranks are forged
early 4age rods (40mm)... they're lighter than later years (yes, smaller.... but when a rod breaks in a 4age, it's because a bearing failed first)
aftermarket (stock bore....) higher compression pistons
smallport 4age head (maybe polished..... you don't want to port them unless well over 200hp..... and even then it's debateable if it's all that beneficial)
maybe go with a 1mm oversized valve
trd valve springs (those really aren't all that much cheaper than stock ones)
bigger cams (something around 272, maybe a littler larger)
adjustable gears
200mm flywheel (billet steel one would be nice)
then you would want to go with some sort of engine management..... i would at the very least reccomend something distributorless..... less mass on the drivetrain and easier to tune. I really plan to do something very similar to this on my next engine build (ie, my next car....)