The factory manual is the ONLY manual to use for OM603 engine work - period. It's on the factory CD-ROM manual set. The paper manual is out of print, but here's one on eBay right now. I use both, as the paper is MUCH nicer for general lookups, and I check the CD to see if there are updates (there are on some things) :
http://cgi.ebay.com/ebaymotors/ws/eBayISAPI.dll?ViewItem&item=2420732954
The 86/87 heads are flawed and prone to cracking. The 90-95 3.5L heads are reinforced and shouldn't crack. They ARE interchangeable. The 3.5 uses different prechambers & injectors (inclined injection, instead of the 86/87 vertical injection) but just use your 86/87 injectors & prechambers on the new(er) head. You do NOT need to get the 3.5L injectors/prechambers. The 3.0L prechambers *may* need to be lightly trimmed, as mine did, but that only happens on maybe 1/3 to 1/2 of the newer heads with old style prechambers. Worry about that later.
No parts places (Rusty, FastLane, IMPCO, etc) offer rebuilt heads for these cars, you have to buy new ($1600-$2000, bare) or used (good luck finding a used 3.5 head, and they are still ~$1200 at most yards). I know someone who has a rebuilt one for sale right now, fresh valve job, decked, pressure tested, crack-free, etc.... email me and I'll send you his contact info.
As to the R&R job, no it's not rocket science, but it IS extremely time consuming - particularly if you don't have the right tools. There are a few special tools that are a good idea to purchase (probably $200-$300 total) which will make things easier. You can always re-sell them on eBay to recoup some cost if you don't plan to ever use them again. Or you can waste lots of time fabricating Rube Goldberg methods to perform the same jobs, which will probably work, but IMO isn't worth the loss in time (unless you have lots of time and little money).
Good luck,