3SGE 02/90 Rebuild needs help

StopLeak?  Stop Flow more like it.  Once the motor and box are out, I'd be doing a garden hose cooling system flush, perhaps even removing the radiator and having it checked.  While it's apart check the clutch/flywheel (of course).
 
Is there any history on the vehicles servicing?  How long ago was the timing belt done?  If there are already issues within the cooling system it's probably false economy NOT to replace the water pump.
 
As far as budget tuning goes, a tidy up of the head while it's being done would be reasonable.  A good way of having more fun on the road is to focus on the handling - replace all the suspension bushes (TwosRUs do an amazing full kit for a surprisingly small cost), and make sure you've got good tyres and a spot on alignment.
 
Don't be tempted to remove the standard intake piping and throw a podfilter on it - other people have tried it, only to find that Toyota did actually now what they were doing and the standard system really works!
 
Perhaps check the catalytic convertor?  A good hi-flow cat and exhaust system isn't overly expensive, and should show good gains without being un-neighbourly as far as decibels.

I belive that 3SGTE clutch and flywheel is bigger. Theres not much performance wise that can be done to the 3sge without spending big bucks. Like Dennis said a nice exhaust and high flow cat

Little bit (actually, a lot) concerned when I read your comment about the flywheel.  Given the speed at which these rotate lightening isn't a job for an enthusiastic amateur with a 4" Hitachi.  Do have it seen to, please!
 
Good to see you're replacing the radiator.  Don't overlook the coolant pipes that run from the stern to the bow and back again.  My suggestion : while the engine (and the radiator) are out, use a loop of hose to connect the two engine bay ends of the coolant pipes.  Block off the lower radiator hose end, and then fill the pipe "loop" with a 50/50 solution of vinegar and water.  Let it sit for a few days, then start flushing the loop until it runs clean.  Also, while the loop is internally soaking remove the underbody shields and inspect the two pipes for corrosion.