03 90hp 2 stroke runs great has started a problem of when its warmed up about the third or fourth start it apparently quits firing.When it cools down it will crank.

After warm-up. Does engine crank over with no spark or will it not crank over period?
If cranks with no start
Check Ignition system - Use spark checker.
If no spark check Stator, Trigger & Switch Box.
All three can be effected by heat.
Stator is most common.

Replaced CDM Module on #1 cyl has cranked ever since.Went ahead and replaced the other two just in case

Good that you replaced the other two.I hope the problem is solved now.If have further any problem ,then do tell us.