Yep, you're correct about the C/R. I just put a 97 vortec 350 in a 91 SWB truck and haven't had any problems. I used the stock V6 computer and a GMPP intake for TBI. What type of lift are you running on the cam? Anything over .475" will cause problems. You'll get coil bind from the valve springs and pinch the oil seals. The push rods will also hit the oil drain back holes and rub a hole in the push rods if you don't drill them out larger. Trust me i've experienced with a lot of these engines and that's why I'm converting to an LS1. I broke a valve spring with too much lift on the cam and roller rockers.

Is the knock in the upper or lower end of the motor?
Is the knock only during start up?
What type of MSD ignition do you have?
Did you use the vortec roller cam and roller lifters?
Did you keep the original 90 block?

I bet we can find the knock.