I would pull the plugs to see if any cylinder is odd looking. Since there was a rebuild here, they all ought to look fairly even, with some variation in plug color due to mixture variations. But no cylinder's plugs ought to look that much different. Then a compression test. These 2 checks are good to (maybe) point to an exact location.
Other possibilities:
- Perhaps a slightly sticking intake valve or one hanging open a bit.
- Could be valve train stackup with milling on the heads and a long pushrod hanging an intake valve open slightly.
- Or the clip flew out of one intake lifter and it has pumped way out, hanging the intake open.
- Electrical misfire in the distributor (crossfire) or crossfire on the wires
- A cam timing issue, but the engine would not likely have jumped time that badly assuming a new chain was used.
OP, can you tell us:
- New timing chain & sprockets?
- Was any head milling done? Any valve work done?
- Original pushrods used?
- What rockers do you have? Stock stamped ones?
- Was cam lube used on the cam and bottom of lifter when installed?
