If that is all you got in lift then it wasn't a 3" lift. As you already seem to have calculated. 3" should measure 3" after installation not a fraction of 3". I also am looking at the body lift, but like VXorado I prefer to find out how to do a project and then do it myself, so I will be installing the 1" body lift. That should give me the clearance I want before I go matching the size of tires up to my VX. The body lift does make a difference, but as stated and discussed many times in previous posts the tire and rim make or break the entire set up. Some combinations don't rub and others do. I have not invested to much time in this subject because I am not to that point yet, but I will be researching that when the 1" lift is complete.
Right now I have P265/70R16 Geolander tires, and with the offset they stick out a little less than your tires appear to. I saw the other pictures you posted showing your day wheeling and the tires appear to be a snug fit. I would question the 3"lift because it looks like I have the same amount of room or more after my lift than you ended up with, and I didn't go for 3" only 2". I wish I would have taken measurements before and after but I didn't. I did however notice that my bump stop was just about resting on the rear axle. now I have tons of room before it will contact the axle. I think I will crawl under and measure to see if I have 2" and let you know if that will be of any help.
Good luck in figuring out what to do next.