rough running on 1st start up of the day

That's a good number of hours in 4 years! Can you isolate the problem to ignition or fuel? Is it worth heating the ignition modules before the first start to see if that makes any difference?

Can you look in the float bowls to check the fuel level and the free movement of the float needle?

You could do a cold leak-down test to see if you have a non-sealing valve.

Try turning on the boost pump for just a few seconds before cranking and see if that helps.

Hi Sam - I just said that and a few other questions - all lost due to Error!!

To clarify a few things. I am based in So Cal the ambient temps are 70f and above when I start up. I do run the boost pump for 1-2 minutes before starting. I will take a close look at the float bowls during the 100 hr. inspection.The valve concern is possible, my last several (warm) leak down test have revealed the #3 cylinder about 5-8 low, maybe it is getting worse.

I will try and duplicate my lost content.

Have you been observing the Rotax recommended spark plug replacement interval?

What fuel (ULP/AvGas) are you using?

"run the boost pump for 1-2 minutes before starting."

Yes but do you observe a pressure rise or the sound of the pump slowing as it reaches its max pressure?

Your annual hours are high by most standards - have you considered reducing the 5 year (some particularly in the carby area) rubber replacement, in view of this?