Subject: 90-93.
Question:

Would a 93 eclipse's transmission layout (manual) be compatible for a swap inot a 90 (auto) Eclipse?

Answer: Robert,
A '93 transmission/flywheel set up uses a 7 bolt design, while your 90 Eclipse uses a 6-bolt configuration. If you really want better compatibility, it would be best to use an 89-3/92 Eclipse, Talon, or Laser, 2.0L model.
Anthony