Front housings on kicks are aluminum, rear is steel.
You aren't going to be messing with any splines at all, other than axle splines....
The drive shafts are going to unbolt, and bolt back to different pinion flanges, so you can't put them back either..
So, the word "splines" is confusing here.
The only thing you are really going to be messing with, that requires it to go back together just as you took it apart......... is  NOTHING REALLY!!!  ÂÂ
If you are just swapping in thirds...... drop the driveshafts by unbolting the flanges don't even take them out... SO.... you don't have to worry about them.. they will only bolt back up to the pinion flanges two different ways, 180 degrees out... er... maybe they will bolt on four ways.. it might be square.. BUT the point is, it's the flange, and doesn't matter... iand the pinions will be different, they don't care which holes are bolted to the driveshaft. You have to worry about that alignment only if you have a slip shaft, and you can get the U-Joints out of phase, you can't in this case.
The splines in the axles are going into different side gears in the different thirds... so you can't realign those splines.. and once again, it isn't balanced that way, so no difference in how you slide the axles in.
Hmmmm.... I am having a hard time thinking of ANYTHING on a simple 3rd member swap that has to go back with care on original alignment..
am I daffy here? did I forget something??
This is a simple straight forward swap... except the losing of the rear ABS Sensor..
not to mention it depends on a 89 Tracker even HAVING the 5.62's in the first place.. a REAL long shot.. most wrecking yards I have talked to have not even HEARD of that ratio..
One thing at a time. Get the gears, come on back and take it one step at a time. There are no great mysteries on a simple 3rd member swap, and once you do it, it will all be clear as day.