So yesterday I observed that Dragon's Lair was ignoring some command strobes (actually a lot of them) and just staying in input mode during this time. The result was that after a successful seek, the AVR would read back codes like 0xD0. I guess the real LD-V1000 had some pull-up (and/or pull-down) resistors for handling this scenario which I probably ought to implement.
UPDATE: Looks like my LD-V1001 won't play discs anymore, or even respond to play. That means all it is good for is comparing strobe timings :) I guess this gives new motivation for me completing my project! Hehe.