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Is the B&M flex plate supposed to make up for a converter that is built for an internally balanced motor?



yes
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For some reason I am still having trouble with this because I think all cranks are balanced by the manufacturer? At least all 383 and 440 cranks I have seen have drilled balance holes in the counterweights. I am thinking its dynamic balancing? I am no expert on this but thats always what I have assumed?



Yes, cranks can be balanced to themselves. However, we're talking about the whole reciprocating assembly of crank-pistons-rods; that's a different balance.

Consider a rim, one that's perfectly balanced. Now put a tire on it, one with a big chunk of steel stuck in the tread. Unbalanced, right? Now, put a balance weight opposite the steel to bring it back in balace as an assembly. That's what externally-balanced engines are. Balance weights are placed on harmonic damper and flywheel/torque converter (by OEM, anyway).
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I also thought that the torque converters were balanced totally separate from engine? More as an aft of the crankshaft.



Yes, converters will be balanced unto themselves, and these will usually be thin weights, about 1/2 size of a stick of gum. 1-2 per converter is common. The balance weights for an 'external-balance' converter, though, will be ~1" long and 1/4" thick, usually one each side of the drain plug.

Here's an old thread, it's on flywheels, but there might be a nugget or 2 of info that will help you.

https://board.moparts.org/ubbthreads/show...&PHPSESSID=