If you switch to bigger injectors without making a corresponding change to the cranking fuel table, you'll increase the cranking fuel by virtue of the bigger injectors. The cranking fuel table like other pulse width based tables have to be calibrated independently.
Long cranking times on the C3I ignition should be limited to how long it takes for the C3I module to receive a cam pulse so it can sort the trigger pulses from the ECU or the crank trigger. Having the right fuel and the right air bypass is key to short cranking times. The XFI can also mimic an accelerator pump on a carb if you pump the gas pedal when cranking. Pumping the gas pedal will cause the ECU to pulse the injectors. If this helps, you can make corresponding adjustments in the cranking fuel table. You can also crack the throttle when cranking to see if you need more bypass air to shorten the cranking time.
I typically observe the injector pulse width on a properly calibrated, tuned, and warmed up engine during idle to establish a baseline cranking fuel at 2 to 3 times this amount.
The other thing is to wait a second or two after key on before cranking. This gives the fuel pump time to build pressure to a nominal level. This is a habit I picked up since I had a new 1985 GN which seemed to start better doing this. Before, with a carb, I used to just switch from off straight to cranking... This doesn't always work so well with EFI whether factory or aftermarket.