The 91 A4LD is different. The 87-89 A4Ld's only have 1 solenoid on them to lock the converter. The 90-93 A4LD's have 2- 1 for the converter, and the other is for the 3-4 shift.
The valvebodies are slightly different as noted above. Your 88 will not have the wiring or the computer setup to properly operate the 91 trans.
Yes, the 91 will bolt in. Not sure if you can just swap valvebodies.
I did just what you are doing to an 89 notch, but I ended up with another 2 solenoid valvebody. I bought the ATSG manual and the update supplement, just to deal with the change, and it paid off.
Someone on here tried that change, and it sort of worked, but if you are going to the trouble of changing trans, you should get one that actually fits.