6 sp crashes going into 2nd gear
Kevin, in 17 years of ownership, 4 Miatas, the issue you describe, it is more often failing clutch hydraulics. Usually the clutch slave, but it is cheap enough and easy enough (and highly advisable) to replace both the slave and master at this point. It will eliminate two failure points at the same time and reset that system in terms of maintenance.
Many people try to fix the issue with fresh transmission fluid, bleeding the hydraulics, messing with the clutch pedal adjustment, or rebuilding the shifter. My experience has been the hydraulics are likely the resolution.
Because you describe the pedal needing to be held deep and longer, that is a key sign to the hydraulic components weakening.
The braided line in those kits is worth every penny. It makes replacing the slave considerably easier and eliminates the failure of an aging, OE rubber line. My 10ae, a California car it’s entire life, had the rubber clutch line rupture after 13 year and 160k miles of use.
The other possibilities to crashing gears are worn synchos, bad engine mounts, or broken shifter bushings.
Good luck.