Just playing devils advocate here.
I know you said an sye is at the top of your budget, but then you follow up with “I want to do a 4 inch lift a year or two down the line for an overland build...”.
Begs the question. If an sye is inevitable and you’ve got the budget (even on top end), why not do it now? Even if you have to save for a short while. The cost of removing a lift will just eat at the budget of your future plans.
An SYE will require a new driveshaft...I was going to ask if the driveshaft length needed to change but I went ahead and did the math....technically yes, but by about 0.2", so he should be fine, especially if you tell Adams or Tom Woods or whoever what your plans are.
That said,
and I'm looking for somebody with more expertise than me to correct any misinformation, going to a DC driveshaft will likely require a different pinion angle than the slip yoke driveshaft. Maybe he's currently in a good range, maybe not. It could require adjustable arms, too. This is one of those things where it can be hard to do it piecemeal; every new component requires another new component to compensate. But it's really worth it.
For the skid plate drop, if you don't have a transmission jack it can be a bit of a balancing act, and if you go so far as to remove it getting it back in I found to be a pain to align & for getting at least 2 of the bolts back in. This is what I think I would do, with the caveat of I've never actually done this so YMMV:
* loosen all 6 bolts so that there is a 1/2" daylight between the skid and the frame.
** if you want to drop it further than that, you may end up needing longer bolts
** if you do need longer bolts, change ONE bolt at a time, and you won't have any struggles aligning the thing
* take one bolt out, add your spacer washers, put the bolt back in
* repeat for all 6 bolts
* tighten everything up
I don't think you'll need to loosen the 4 nuts for the transmission mount, but it might not hurt.