Need some tech help!! Please!!

wondering if anyone can help me out, car sometimes feels like its running on 7 cyl. starts stumbling and backfiring through the intake and exhaust, not all the time though , thats whats weird!! sometimes it runs great then all of a sudden it does it again, when I push in the clutch and take the load off it seems to go away, as soon as I let up on the clutch it does it again, Please if someone can help troubleshoot this I'd appreciate it!!!
just rebuilt the motor about 1000 miles ago, no major mods like heads, just intake, tb, cam, exhaust, maf, can't figure this one out, checked my cap and rotor, made sure all the wires are tight on the plugs, any help would be great!!, Thanks!!