Sorry to pile on and you may have discovered this already, but it appears your repro playfield is missing the slot for the shooter lane switch. There have been a handful of people posting about this recently. Just didn't want you to get too far populating before you noticed.
I will say I did a Whirlwind swap with a CPR playfield several years ago. Aside from some suspect dimple locations, it went smoothly and had no issues with the clear. Sounds like others were not so fortunate.