i have a clifford as well, never had a problem. but they are complicated and if they start to play up i can imagine it being a headache. proximity sensors can be adjusted, so i think its all good
did you prime the engine before starting? it takes a good while turning over before the engine is ready to start ( best way is to remove efi fuse) just make sure you do it on the new one. I always do it if i dont start the car for more than a couple of weeks.
Its not just about one of the rear wheels rubbing. If its not rubbing, its still out of line and your car will be crabbing because the rear wheels are not in line with thr front. If your going to lower your car do it properly
Long term effects are the turbo is put under a bit more strain and if your putting your foot down at low rpm then the clutch will be put under more strain as well. If your doing high mileage then just leave as they come in terms of tuning. as you have noticed they start playing up because these modern diesels run high pressures Egr delete keep oil cleaner for longer and car smokes less as well when standard.