As far as bellhousings go, I believe if you get one with a "T" as the third digit in the part number, it'll be too deep as it's a truck part. I'm not sure if there were any 4-speeds offered for SBFs in trucks, so I may be off base. Of course if I'm wrong, that it's actually no problem as you couldn't mess it up, now could you?
Now another thing to look out for as far as the toploader itself goes is, tailshaft length and input shaft length and input & output shaft size. Galaxies and other big cars and trucks have the longer tailshaft, so you may need a shortened driveshaft. Most of these longer housings have multiple bosses to move the shifter forward however.
www.4speedtoploaders.com is David Kee's website and has breakdowns on part numbers and such.
The FE powered trucks that had toploaders had the deeper bellhousing that required a longer input shaft. If you have one of these and they did make a deeper SBF bellhousing, this might be the easiest solution, although the better one would be to have the tip of the pilot shaft shortened (this is what's longer). If you decide to go to a steel scattershield (I recommend), you typically have to clearance for long tube headers and sometimes the clutch linkage. Usually these go for around $100 on Ebay and if they're modified, the SFI rating on them is no longer any good (and it's only good for a couple of years anyway).
There are big input/output shafts and small input/output shafts. The big I/O trannies came in BBF powered vehicles and the small I/O typically came in small block vehicles although the 390 toploaders are small I/O trannies. Typically the big I/O trannys have a 2.32 first gear ratio called a "closed ratio" tranny. The small I/O trannys typically have a 2.78 first gear ratio and are called an "open ratio" tranny.
As far as clutches go, I prefer the long style clutch and the stock z-bar setup. Some guys like the diaphram clutch and the cable setup. It's more preference than anything I guess.
David Hearne aka D.Hearne probably knows as much about Toploaders as anyone on this board, hopefully he'll chime in and put in his two bits.
GP001 is probably the most experienced when it comes to putting in a hydraulic clutch if you want to go that route. He has a pretty slick setup on his 6-speed tranny. He also used a scattershield.