pslmotorsluke

Should be fine.  Our general recommendation is to keep internal temp below 70°C

Unfortunately your ECU is one of the earlier ones which had more basic trigger scope functionality so we cant see ther voltages or waveform to get a good feel for what is going on.  
But the firt thing I would try is just reduce the arming thresholds a little on trig 1 & 2 to see if that makes any difference.  
Try something like below.  If that doesnt help I think you will need to get someone with a standalone scope to do a capture at high RPM.  Or possibly you can borrow a newer ecu off someone to use the triggerscope function.