Bypassing the j-tube is just needed to get rid of restriction when using a adjustable fuel pressure regulator and fuel pump up grade.
As far as the upgrade to rum more boost, the lex/550 combo is probably the cheapest, but doesn't have as very clean idle. There is more than one way to go to a MAP (manifold absolute pressure) set up. Ex. HKS Vein Pressure Converter (old school, but has a chip to work almost plug and play with 550cc injections), MAFT Pro (I have heard some bad things about this system on other cars, but I don't know about it for the supras), Map ECU 2 (which is what I am looking into), etc. They all do the same thing, they take a MAP signal and convert it to a frequency used to read the Karmen Vortex set up on the 7mgte ecu.
As far as EMS programs, I am pretty sure toyota has made it difficult to crack our ECU's.
Also tsuper92 mentioned a boost cut controller, this is not a very good idea unless you are monitoring everything such as afr's very closely. Toyota but fuel cut there for a reason.