what was the exhaust before? you now have a hi-flow, have you leaned it out too much?

put the old plug wires back and see if the prob goes away - at least you can determine if it is plug wires or exhaust.

when doing the work, do you knock anything loose (vac line, wire, etc?)

check plugs and wires - all ends on tight, no arcing, etc? no cracked plugs? dist cap OK? wires seated in it OK?