Acceleration cut at 5k rpm
 

Today I changed the oil on my miata. While taking it out for a quick ride. I noticed a clicking when I press the clutch and it will cut out at 5k rpm and stop accelerating. I noticed when I got back home that the clutch rubber stop was in pieces on the floor. Would this be the cause or should I be looking somewhere else? Car is a 99 running on a ms3 with no turbo.

Depends. If you use the upper plunger for launch/flatshift it needs the rubber to depress the switch otherwise it just slips through the rubber mounting hole. Without it megasquirt thinks you are constantly shifting and will set the limiter to the flat shift cut RPM.

This is exactly what I was thinking.

Mine just did this in the middle of a track day which prevented cruise from working, I just put a bit of duct tape over where the switch pushes for a quick fix, been fine for a few weeks.

A couple of pennies taped to the pedal works well too