I've done the powerstroke on hotair conversion. Don't worry about the pipe length, there was no difference in spool from hotair form to powerstroke with 3" piping.
You will have to move the throttlebody to the pressure side as close to the intake manifold as possible or throttle response will be aweful. Use an 87 style inlet bell on the intake of the turbo to mount the MAF pipe directly to the turbo. Put the throttlebody in the intercooler piping right before it enters the intake. I coupled it to the intake using an inlet bell bolted to the TB and coupledd with silicone hose. You will have to use an 87 throttle cable or FWD cable from the junkyard to get the length you need. Flipping the IAC housing around will help clearance also.
I have a TA64 in the 87 housing clocked facing forward and into the intercooler. From the exit, it runs along the drivers fenderwell and 90s over the brake booster, into the TB and then into the elbow welded onto the back of the intake.
Spearco sells an elbow that will bolt onto the back of your intake manifold but it's only 1.8" at it's smallest point and the bend is pretty sharp. I found a cast 3" elbow with a nice radius at a scrap yard and had it welded to my intake. With a slight backwards tilt it clears the turbo.
As for the manifold itself, your biggest gain is opening up the ports. It's been in the 10s in hotair trim with only a port job and I'm sure can be pushed farther with an intercooler. I ported mine to the felpro 1200 gasket which required welding material to the runners. Later on I cut the top off and gutted the inside making it an open chamber but by far the biggest seat of the pants difference was from porting the runners.
It sounds like a lot but I spent $30 on the mandrel 3" piping bought from a muffler shop. $120 in silicone hoses and good clamps. I'm sure you could go with rubber hose and hose clamps much cheaper for the challenge. The elbow was free, welding the intake was $50, porting was done in the garage for free. You could probably do the whole thing for $350 including the price of the intercooler if you really try.
Once you open the intake, get a decent sized turbo, intercooler, and get a good downpipe, the hotairs will run the same times as a similarly modded 86-87 car.