So, an update:
After getting the calibration properly sorted, I started adding mods back one at a time.
First the Johnson Rods went back in. All good - I could use all three heights with no problems.
Then the rear Proud Rhino spacers went in. Still good - no problems
Then I added the rear limit straps. Since I am running mine in a different location than recommended (and really, I don't see how you could run them in the recommended location at all - see earlier post for info) I wanted to make sure they weren't binding somehow. Still good - no problems getting into any height.
Then the fronts went in - ah-ha! Now I've recreated the access height problem. I know the suspension can drop lower than access height before hitting the bump stops if I use the GAP tool to deflate the struts, but when lowering to access the truck thinks there is an obstruction and bounces back up to extended mode - just like before. I can only assume it's going down too slowly for the last few mm which causes the computer to think it's not going down at all and trigger the 'obstruction' error.
Given that I don't actually use access mode unless I'm loading my tent on the roof rack, I'm not too concerned with this and will leave it be. Further, I have the LLAMS tool enroute, which should provide a work-around for this should I need to lower the truck.
Over all, I can't say this kit is a home-run, but with my 33s it's pretty important to have something like it. I think the better solution might still be to mod the struts themselves. Something I may try eventually.
I would like to hear from Lucky8 if they happen to read this concerning how they are mounting the rear limit straps without major rubbing, and if they have a solution to the access height issue. Anybody listening out there?