Ive looked into going NA-T myself. different people use different set ups. i know the whifbitz setup uses AEM but i think Greddy Emanage Ultimate is a cheaper option (from what ive seen or unless you get 2nd hand unit). its not on ebay.uk at the moment but ive seen emanage ultimate going for 350GBP with harness (listed as new).
why are you upgrading the fuel pump? the injectors wont run much higher than 330cc, most starter set ups run the standard fuel pump and dont have any problems, over 350bhp your need injectors, on which case you have a variety of sources. but def do your research, cheap injectors arent worth the hassle. 550cc is the best start upgrade unless you want 500bhp. 2jzge injectors are TOP FEED u cant use 2jzgte ones. they are listed as high resistance, 12.5ohms should be fine. you can get rx7 turbo II injectors, they are 550cc high impedance and drop right in. if you do upgrade injectors, u can use a stock TT denso pump instead.
the intercooler from the GTR shud be a treat but you can get some amazingly cheap intercool kits for the 2jzge if you look hard enough.
why do you want to swap the head? what is the reason for making extra work for yourself? if its a project then fair enough but for power gains you'd be better spending money on boost. you cant just put a gte head on a ge. theres a things you need to do, check this thread on SF: http://www.supraforums.com/forum/showthread.php?225971-NA-to-TT-Conversion-TT-head-swap-info
what are your power aims? its best to try and use power targets or finance options to make your build around.
its common to see 2jzge-t running 300bhp to 350bhp with a standard headgaskett. i spoke to a tuning garage and they said its best to go with one anyway. 1.3mm on the 2jzge will lower compression down to 9.2:1 allowing 350bhp+.
most medium sized turbo's should run without hitting the distributor but the main reason for using coils when going na-t is because it sometimes gets in the way, this isnt the only reason people swap to coils but a main reason its so often talked about when putting a turbo on these sexy engines.
im not 100% sure on the wastegate, you could get a bigger wastegate, cheap XS kits use 46mm and the Whifbitz kit uses 45mm, where did u get 38mm from?
you can spend THOUSANDS on an intake manifold. i had a quick look and find some "amazing" but very expensive set ups. you can hit high power figures with the highly effective inlet your using. again, need to ask why you'd want to do this.
people on NA-T forums reckon most power running through a w58 gearbox is 450hp and if your using a stock clutch or even auto then it wouldnt be a good idea doing drag starts constantly.
you also need piping from wastegate into the manifold, but if your doing all that custom then im sure your tuner can sort it. you dont want to be venting, screamer pipes are evil
ive tried to use information ive read on NA-T's im not saying its 100% just trying to be helpful. :-)