2000 baja 342 boss with 502 efi just changed dist cap /rotor cap /plugs and cleaned thottle body now the port side engine is running about 500 rpms less than the starboard side and is toping out about 3200 rpms in gear out of gear it will rev to 5000 rpms the starboard side is running ok engine was running ok before just wanted to tune it up

you got the firing order wrong

The first thing you might not want to rev it to 5000 in neutral. Can you say boom! Firing order sounds like the problem. Def will not let it rev up under load.

1-8-4-3-6-5-7-2 Make sure you got the plug wires routed correctly and make sure all the boots are on both the cap and plugs tight. Listen and feel for the snap.