The tube from the AFM to the turbo is commonly referred to as the accordion hose. Someone found a nice inexpensive replacement and posted it on here a while ago. Try searching the forum for "accordion hose" and look for a thread specifically about replacements. I'll see if I can find it for you.
40psi above 3K RPMS is within spec (36 to 71 is what the manual states... never seen above 60 myself and that engine was not stock at all). Above 4.3 is all that's required at idle. Not a high pressure system... it's more about flow. It's in the TSRM in the Lubrication section:
http://www.cygnusx1.net/Supra/Library/TSRM/MK3/ <---- save that link!
On the Turbo the only thing you really need to move is the 3000 pipe, the rest can be worked around. On the N/A you need to move the throttle body, don't worry about disconnecting anything but the 1" tube connected to the front of it and the throttle linkage, then just flip it up over the "Y" pipe.
ARP is the most requested replacement for the head. The OEM bolts are reusable too, but I'm not a fan of reusing 22 year old bolts for anything. ARP offers both bolts and studs. Studs cost a bit more but offer more clamping force. For engine's that are mostly stock bolts are more than sufficient, just not at the stock torque value. Bolts should be torqued to 75ft lbs and studs to 90ft lbs. Do NOT over torque them, lubricate the threads very well with a good moly grease and ALWAYS chase the threads in the block.