If your mounts are off by too much, your rear end won't track straight and you could experience vibration from having an incorrect pinion angle. Your best would be to get the brackets tacked into place and them mount everything up and double-triple measure all of your brackets and angles and verify that everything is okay and there are no interference issues when either side of the axle travels up/down. Something else to think about/take into consideration, the 8.8 is a little narrower than the D35. I would suggest using a digital angle finder to help get everything dialed in. I only had adjustable uppers and I was able to get everything to work out pretty well.
I know that when I did my 8.8 swap a while back, I had issues with the diff cover coming in contact with the skid plate for the fuel tank, but it was an after market side plate and a pretty thick diff cover. This is where taking the time to mount in the jeep before welding everything solid really would have helped.