Basically, here's what I spent:
$300 — tranny kit from boneyard (transmission, pedal assy, flywheel, clutch, driveshaft, rear cross member and other odd bits — had to pull it all myself too)
$150 — modify and balance driveshaft
$70 — new master cylinder
$80 — new slave cylinder
$140 — new clutch disk
$100 — new pressure plate
$10 — new pilot bearing
$65 — new release bearing
$20 — resurface flywheel
$25 — rental of transmission jack to remove a/t
$955 — TOTAL

This doesn't show any costs for modifying the crossmember because I did it myself. A welding shop might charge $50-$100 to do the mod.

Of course the decision to use new hydraulic components and a clutch is up to you. I might reuse a clutch because it is easy to see how much life is left in it. But, the master and slave cylinders are such a PITA to replace, I'd always stick new ones in.

Personally, I believe the tranny was overpriced. It has a LOT of wear and the car it came from was trashed; nowadays, knowing what I know, I would have offered $150 for the lot understanding that there are plenty of better transmissions around, you just have to look for them (FWIW, since then I've bought entire cars (one with a running engine) with manual trannys for $400.

How much money do you have and where have you been hiding? 5-speeds that fit the M110 or OM616-617 engines are ultra rare. Search the forum for more info. Why a 4 instead of a 5? I'd guess that it has something to do with the US national speed limit only being 55 mph when these cars were manufactured. Hell, you could barely get out of 3rd much less need an overdrive 5th back then. The only stock 5-speeds in 115, 116 123 or 126 chassis you'll see in this country are gray market cars from Europe, not vehicles exported for the US market.

See answer to #1

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Never a dull moment at Berry Hill Farm.