Chickenman nailed it. You pretty much have to start over. These old engines are prone to knock especially in cylinders 5&6. Modifying the head with a coolant bypass (as discussed in one of the L6 stickies) may help a little but with pump gas I bet it still knocks like crazy with any kind of real boost. If you end up starting over, I would start with a decent running NA engine. Once you get it set up and running good, then spend the money on a fancy turbo build. That way if the blow up the NA engine, there is less money lost.
Oh, and by the way triple weber setups are cool! Alas, more power is addictive and I get it. I caught the bug back in 2008. But unless you're racing, a finely tuned NA L6 is more fun to drive on the street IMHO. A lot of the power my car produces just ends up going up in (tire) smoke.
That's my $0.02. Good luck.