Show your work. Where you're going to even get a high mileage used automatic transmission for an E39 for $100 is beyond me.
If I'm not mistaken, a manual swap requires at the very least the clutch/transmission assembly, the gauge cluster, and a canbus unit to spoof readings from the AT to make the ECU happy.
Hey man it's your money and your car, you can do whatever you want. Best case scenario you prove me wrong. I personally would not bother, if you want my personal opinion, I think that you're going to go into this thinking it's going to cost 400 dollars and be in for a not so nice surprise when it ends up costing way more, or even better it works, but every light on the dashboard is telling you the world is ending, even with some coding. I know E31 auto->manual swaps are a nightmare, and a quick google search makes it look like the E34 is the last 5 series that you would want to even attempt this on. I'm not sure I believe your $400 of parts figure for what it's going to take to put a manual in, so again show your work.
Again, maybe you'll prove me wrong, maybe you won't, but I don't see the point because IMO your best bet is to pick up a used working automatic transmission on ebay, install it, and flip the thing for a profit. If you really bought the car for like 450, you could probably sell it for 3k or more, and the money you make from that is enough to buy one with a manual unit in it. Your call. Dollar for dollar it makes more sense to not bother doing the swap unless it's for bragging rights.
Lol, didn't mean to rile you up.
I would be getting parts here (all 3 locations are within driving distance of me), parts list with prices:
Price List | Harry's U-Pull It
There is no shortage of manual transmissions there any time I've gone (since I can use e46 5 or 6 speed manuals).
ECU I can flash for free, though you don't have to do anything on the e39
stock cluster is fine with a free flash
^neither is difficult-- just remove the autotrans from the VO, add the manual trans, reflash all modules.
trans is $100 post core return for either manual or automatic. They don't care if the core is manual or auto, as they just want it for the scrap metal
If I'm doing a manual conversion I also need
drive shaft ($20)
diff ($50) (not technically a need, but I dislike aggressive gearing)
slave cylinder ($10)
master cylinder ($13)
shift boot ($5)
clutch/pressure plate: $16
Total: $247 for used parts
While I'm in there I'd also do rear main seal ($27), selector rod seal ($15), input shaft seal ($27), pilot bearing ($20), and throw out bearing ($55) with new parts.
^all new part prices from husker BMW parts if you want to check them: https://www.bmwdirectparts.com
Total: $144 for new parts
Total for project, used and new parts: $391
Hopefully I have sufficiently shown my work.