When I first did this I simply left some of the remaining gear in place and made a nice plug that fit into the hose before the check valve and clamped it in. The check valve should keep it from leaking out as long as you leave it in but I wanted to be extra sure. I can't remember exactly how the h-pipe hooks in anymore since I just welded a plug into it, you could weld a cap on it and cut it right behind the cap when you sell it, probably only have to cut 1/8 of an inch off it to sell it. Did you get the ford smog delete or another? I actually measured some stuff up after I had a belt take some damage at the track and the pulley on the Ford unit is set about 0.100" too far out. I bought another and it was the same. I think I need to do some machining to get it right.
Remove the lines that go to the back of your heads and plug the holes with thermac plugs. You can take the bolts that you removed to a hardware store to find the thread size for the thermac plugs. Also remove the tube going to the h pipe and weld the hole shut. If you leave the hole open on the h pipe it will sound like crap.