Is it possible that the signal from the distributor to the ignition module is too weak due to the extended wiring.
Possible voltage drop due to the length of the wire?
Or possibly a damaged ignition module.
I use a cardboard template to check for clearance. Make the template between the engine and the wheel arch/chassis rail. Like an Engine plate. Then you can hold it up to your spare engine to check for clearance while making the manifold.