The decision to run 1/2 height bushings really comes down to how much that .75 to 1" is worth to you. For me the additional effort isn't worth the relatively small (in my opinion) benefit.
There are plenty 1st Gens using full height bushings that don't have to touch the tunnel with a T56. It's a little tight, but has enough clearance to not worry about.

No bushings :)

besides tunnel clearance what other issues are there when running 1/2 body bushings?

Possibly inner fender clearance depending on how low you go, tire size and how much suspension travel you have...

what about the way the fender lines up with the door? I will be moding the inner fenders for max clearance anyway so that doesnt matter. I didnt buy the DSE front subframe and rear quadralink for the car to sit high. I want it low and to perform to the max

Randy, fenders bolt to the body not the sub frame so they will line find with the doors.

^ Listen to this guy. He's done it once or twice...:D

The bushings also mount to the core support and that supports the fenders, but the manufacturers have that height measurement down so as Rick said you'll be OK.

Edit: Unless you're going for the slammed look, the DSE sub and Qlink will get you nice and low.