Up to now, we didn't even know that also bytes have to be sent.

Benny, we cannot help unless we know in full detail what the micro has to do. Give us a complete flowchart of all procedures, timings etc. When have how many bytes to be sent, when will arrive how many bytes, what bytes are these, how do you process them? How often must the stepper be pulsed per second, how long lasts this pulsing routine, how many steppers do you control, etc. etc.? What else routines have to be processed?

Up to now we can only recommend to keep the ISRs short. But we still do not know, how many ISR routines need to be used at all, if they should have equal priority, or whether a polling scheme is better suited.

Kai