1. The console with a defunct laser system might just have a blown laser. Those get damaged really easily, compared to PC optical drives. The BA chip of the SCPH-39000 series of consoles doesn't get blown so easily, compared to the LA6505 chip of the v9-v11 consoles.
2. Maybe, but it might be because you are using an el-cheapo memory card. My 2 64MB compatible cards occasionally work very well on my SCPH-10000 and SCPH-39006 consoles, but work absolutely horribly on other occasions.... up to the point I think that it really depends on the consoles' "moods".
(And the SCPH-10000 seems to be a bit more temperamental)
Try using a genuine Sony Memory Card.
3. You probably were just working in the wrong direction.
4. Maybe, but it's unlikely. The NA gets connected to the DEV9 interface, which should not affect Magicgate.
Unmodified SCPH-77006 with SM 3.6
SCPH-39006 with M-chip modchip, SCPH-10281 NA and refurb Seagate 80GB HDD
SCPH-10000 v1.00 with SCPH-10190 PCMCIA NA and SCPH-20400 HDD unit