The MERC 383 (58/60) was available with manual shift, so there is your first choice using MERC components.
The 352/390 flywheel will go to a 430 with no imbalance problems. An FE bell housing will go to a MEL block.
I am expecting shortly, a FORD Master Parts Catalog (MPC) for MERC (56/59) and LINC-MERC (60/64) which will help determine exact interchangeability of the two engines components (383/430) and series (FE/MEL).
Both the 383 and 430 are internally balanced, so that should answer your question there. I installed a 390 flywheel on a 430 years ago and there was no vibration problem. So both series must be closely designed together regarding this. There is a contributor here that is swapping a 430 into a '58 FORD (thread below), so you may want to follow his progress. The FE 410/428 are externally balanced so you would want to stay away from their flywheels/dampeners.
I will post what I find in this thread in a few weeks hopefully.
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