Misfire.
To start with, I would remove the distributor cap and check that it is dry inside and then move onto checking the cold start injector was shutting off properly.
Ignition leads on M103 engines are usually good enough (our '90 300 is still on the original leads), but the insulation can crack. Run it in the dark to check that there is no arcing around the leads.

Exhaust.
If it had twin pipes from the factory, it won't like a single pipe in the system, unless you fit one large enough to match the original system's flow rate and there might not be space.

The thumping.
Check that the exhaust doesn't foul the body anywhere when you push it upwards.
Rear subframe mounting bushes are worth checking as well.