Does anyone know of the compatability of these two axles?  I own a '87 jx and found a '88.5 jx rear axle assembly with a detriot locker complete from drum to drum.  Does anyone know if i can swap the third members, brake parts etc..... I want to keep my housing and axles because of diff armor and new wheel bearings and seals.   thanks in advance

Yes, they are one in the same.  The only difference between the two are the outside brake line brackets.

What about the driveline flanges? I know that there is a large and small one, but unsure of the date ranges.  Could I use my current driveline (with small flange I believe) and just press in a fresh ujoint and the flange from this one.    I guess what I am asking is are the u joints also the same between the large and small?

The U-joints are the same, also the same as the Sidekicks and Trackers

Wild

I have 4 88.5 Samurais that have the small flanges and 1 88.5 that has the large flanges.  The large flanges probably came late in the run. 

If you have a large flange diff, you can simply drill the small pattern into the flange.