Got a friend with a 69 coupe, 302 and a top loader. The engine is a swap and he has long tube hooker headers. Everything clears fine. He has the standard gear box though.
Tri-ys come in different flavors. The Shelby knock-offs use 1 1/2 inch primaries and should only be used on mild builds - they are fine for mild builds. On a built motor, or with a stroker, you'll need 1 5/8 inch primaries - which Doug's tri-ys use.