[MC1600]

To answer your first question, it’s start generator, transfer power, disconnect shore power, start engines. But I can’t imagine how any combination of that is affecting your cranking. I’d start by examining the cranking amps of your engine batteries. Just because they’re new doesn’t mean they’re correct. You should not need to use the crossover to start your batteries. Do your batteries have the correct cold cranking amps? Are they properly connected? Is everything grounded correctly?

If all that checks out, I’d start investigating your starter.