MKII, 90-99 NA & Turbo
Verify the noise is coming from the transmission. It may not be, I can tell you the MR2 Turbo I've driven with 50k miles on the odo and 100% stock noticeably rattles at cold start. My LS400 also has a bit of a rattle at cold start. If it goes away as the car warms up it's probably fine.