OK, I fixed the bucking issue. Turns out that when I put in the new 6AL box, I ran the green/purple wires with the others to the HEI. They have to be separated according to MSD because of EMI. Moved them apart 4-5 inches and all is well again.
Still having the other noise. I'm thinking it's either a header leak or rocker arms need to be relashed/adjusted. I'll post back on that when I get under the hood again.
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