I messed with things more this weekend and the problem is definitely that the S5400U doesn't play nicely with SLP/EP tapes, not anything with the tapes themselves.
Here's another 30s sample, this time no funny business like being re-recorded over TV, it's from a 1st gen camcorder SLP VHS-C recording from 2001.
HuffYUV AVI (260MB)
H.264 MKV (46MB)
Based on the visual problems does it lead an experienced eye toward something obvious? Tape tension, alignment drift, fouled SLP video head, etc?
All I've done so far to the hardware is cleaned the Video heads and ACE head with a chamois swab lightly dampened with 99.9% alcohol.
The Funai deck plays SLP/EP tapes just fine, but I'm finding that most of these 25 VHS-C tapes are SLP (makes sense given the limitations of the format) so I'd really rather not use that deck for all of them if I don't have to. So if there are some simple things I should check I'm all ears.