Sorry for the late reply, this was our first time using Link and we had an untested base tune we couldn't verify. I also appreciate all the help and the willingness to dive in.
Turns out it was a simple trigger timing error. We foolishly didn't realize we could have a negative trigger offset and couldn't set the trigger greater than +360. After we had the mechanical timing reference sorted, it fired right up and we were able to go from there.
Thanks for the spark diagnostic suggestion and the calibration correction on the coolant temp we made those changes and some others as well.