The exhaust is an amazing upgrade (I was surprised). The Lexus AFM and 550's aren't necessary unless your running an upgraded turbo in my opinion. The stock turbo has a lot of kick, but its wastegate spring pressure limits it to about 6-8 psi. If you shim the wastegate you can reach 10-12 psi, however depending on your elevation you may be hitting into fuel cut. CT26's are fairly old, small and generally very functional (underrated really). A proper boost controller helps overall if your looking at squeezing out some extra HP from the engine. My car was a totally different beast with the exhaust. I did a Raptor Racing DDP mated to a HKS 3" catback twin tipped muffler system. I removed my cats however because they aren't needed where I live. Cat removal is fairly controversial.. lol.
With the Raptor DDP, it has the turbo elbow integrated. I was going to use a HKS downpipe, but then I needed a turbo elbow and the one I got was the worst weld job in the world. Good paper weight right now.
Also, if your going to go with the 550's and the Lexus AFM upgrade, strongly consider a wideband, AFPR and intercooler upgrade. The wideband is just a telltale gauge to let you know your not leaning out. It doesnt really serve any other purpose than that.
A BPU Supra is generally
550 CC Injectors
Lexus AFM
3" turbo-back exhaust
Wideband
AFPR
Upgraded fuel pump (either Walbro 255 lph or MKIV Denso pump)
57 Trim CT26 (or one of the variants of the upgrades, however there are far better turbos available now.. and deciding on the turbo should precede the exhaust because it may cause you to have to modify the exhaust slightly)
Intercooler upgrade (I got the new DM one... looks good in the box so far. The real restriction is a single "flattened" elbow on the stock intercooler, however the IC replacement only cost me about 450.00 and is a fairly simple install)
With those upgrades you can be pushing 350-400 HP at the wheels fairly easily. (and safely)
Ultimately if you want to build really well, a standalone engine management system is necessary.
All this info is solely from what I did so far with my car and a whole lot of excellent input from these forums. And my Supra is now a rocket compared to when it was stock. (I should note, I am running a Cometic MHG on a fully rebuilt engine with forged pistons... a bit overbuilt... )