I have a 5000XL and work on an E39 on occasion. With the front pad right on the jack point, the rear pad is right before the jack as you mentioned. No issues doing this (yet).
I have a 5000XL too. It works great but my only wish was that the extended tray (the part that makes it XL) was completely flat. One of the corners of the parallelogram is right in the middle of the tray and the jack point on one of my cars is in the same spot. I made a split lifting block and...
I assume you pressurized the air canisters? Mine wouldn't lower unloaded unless they were maxed out. When lowering, mine makes a hissing noise of the oil draining back into the tank.
My girlfriend and I replaced a spring a couple months ago. Getting the right spring was easy enough using the measurement guides in YouTube. I feel like if you have a good set of winding cone rods and don't get careless, it's a very doable job.