[H. L. Chauvin]

Your existing manifold to engine fit & your manifold gasket leak could possibly be "the" problem(s) for at least (2) of the engine's cylinders fed by your intake manifold.

1. Remember, everything is great except at caution lights when the engine heats up.

2. The manifold can heat up & expand; & the manifold gasket can move slightly & start leaking increased "air" at the engine's intake port feeding (2) cylinders.

3. Increased "air" can cause an insufficient supply of fuel/air mixture & also too much "air" in the fuel/air mixture.

4. Remember, pulling out the choke helps the missing engine run a little better -- possibly because this adds more "fuel" to the intake's "air" leak.

5. Appears wise to check "flatness" of the combined intake/exhaust manifold surface & install with a more permanent copper manifold gasket, especially near the coast in areas of high humidity.

Not being able to "see" what you have, just one more "guess" to consider.