Is anyone running a Delta with Johann’s marlin and a Z-probe? Is everything working smoothly for you ? I’m running into issues when my print head is eating into the object during print, and I didn’t notice this with the vanilla Marlin.
Yep, we’re running it @@deltamaker without many issues. We have some changes in our branch though; you can M500 the autoleveling data so it’s saved between machine starts, etc. Did you ever have vanilla marlin auto-leveling working on a delta? I never could get auto-leveling working on vanilla marlin with delta, it always (ALWAYS) simply assumed that it was a regular machine and ignored delta geometry. I’d much rather have a 3-point probe of vanilla branch. 
That’s exactly the problem I ran into. The vanilla Marlin G29 doesn’t work on a Delta. I need to take a close look at my z-probe.
Adding alternate probing setups is pretty easy with Johann’s implementation. You could implement 3 point planar by storing a plane equation from three z_probe and then in adjust_delta plug the xyz coords into the plane equation rather than use Johann’s bilinear math. btw. This is on my todo list. When I get around to implementing it I’ll post it.
I’m using stock Marlin, haven’t messed with the bed leveling yet. As long as I don’t move the printer it stays level 
I think the only issue is ambient temp, which is pretty constant in my basement. Right now I’m working on getting my dual extrusion going, but mostly just busy printing stuff. Even with the faster delta, big things take a long time.
I did have a head crash issue with an old Slic3r - when using dual extrusion and hop sometimes it would hop down twice. Seems to be fixed in the new version, though.
However, you might want to check your gcode still - grep for Z and make sure that it’s monotonically increasing, or at least doing what you told it to