Bob,
Good stuff, I have 2 Toshiba 3960's (one $65 new from best buy, one $16 from ebay), a panasonic S47 and a Toshiba 4960 (all bone stock). All impressions are using units as transport only playing redbook CD's feeding 2 pretty good systems. Sound quality ranking (worst to best) Panny S47, Tosh 3960, Tosh 4960.
I think if the 4960 had come out before the 3950/60 they would have grabbed everyone's attention (although maybe not quite as easily modified with single board) and people would have jumped all over them. I think the cheapskate in a lot us still would have liked the idea of a cheap(er) player like the 3950/60, but I think the 4960 sounds better to start.
The last thing you asked is what other people suggest for future mods, I would suggest mechanical mods in the form of damping the chassis, maybe try some ERS cloth, better power cord. For damping, try floor tiles from Home Depot, duct seal (clay like stuff) and (for transport use) a high quality digital transformer (Lundahl).
As an aside, I really wanted the Panasonic S47 to best the 3950/60, nicer display that tells something, cool looking blue led lit clear plexigas drawer and with a buffer so big that the player continues a full 15 seconds after the disc is stopped (mechanically) while playing.
Roger