Did the problem exist before the new alternators?? Have you verified alternator output voltage and amperage while running???
496 ECM's do not like low voltage at all.
Full charge batteries should be at 12.7v. If they are down to 12.2v after running 5-10 mins

If you are getting a stumble when trimming or tabbing, its taking a power draw from the engines or ground issue

Problem was before Alternators being replaced.
Voltage at idle today was low at stud on back of alternator.
Yes at full charge 12.7
Agree on drawing when using switch but all battery cables including to engine ground are new. Both motors

What is "low"?? Battery voltage? or less than 14? If its in the 13s, your at least getting something from the alternator which means its working, but something is off with the regulator or excitation circuit.. Try revving up to 2000 rpm and recheck the voltage at the alternator post.
Also, do you have a clamp on DC amp meter? would be curious to see amperage output at 2000rpm.
Might also want to check your starter post fuse. I just installed a 105A alternator on my 496, but as part of that had to replace the orange wire in the harness with 4AWG as well as the starter post fuse to 150A from the 90A stock fuse...
You can't just throw a high output alternator on and not change anything.