depends on what kind of power you want to make, how much you want to spend, and i dunno about the auto tranny but the manual trans is said to hold up to about 450hp.
if you go na-t which is the cheapest way for about 350-400hp which seems to be the general kits on the market which go for about 5 grand. then if you do a swap it will run you 5-7 grand depending on what you do and where you do it, will get you 300-320hp? depending on which motor you get (USDM or JDM) but there is bling factor involved in the swap. plus if you want to make serious power, its easier to make it. dont get me wrong though, the na motor if done up can make alot of power. a few? members on this board make in the upper 500 range.
as for your brakes LS400 caliper upgrade is also available. supra is better though.
so it all boils down to how much power you want to make and at the same time how much money you want to spend.