Hi, been lurking the forums for a while but just registered to respond to this.
I have almost the same situation as you. Purchased last September and didn't use the AC until this summer. I am finding it becomes an absolute chore to drive with the A/C on (manual transmission). I like to think I can drive a stick pretty well, but this car throws me for a loop sometimes.
I find starting off in first to be ok for the most part (ECU likely helping out?), but any shift after that the RPM just drops like a rock when the A/C is cycling. I fully understand that the A/C is a power hog on our little 1.5L engine, but it becomes impossible to get a smooth shift without really abusing the clutch to smooth it out and likely abusing the synchros by needing to shift so fast. I have tried reving higher and shifting later and also shifting sooner at lower rpm, but I can't seem to figure this out.
As you mentioned, the worst part is the fact that the A/C cycles, so one minute you are trying to shift at lightning speed to catch the revs as they fall (A/C cycle on), the next the RPM hang as they usually do (A/C cycle off). It really messes with you! Needless to say if you aren't staring at the RPM and listening closely to see if the A/C is cycling at that moment you likely end up with a jerky shift.
I am getting mine checked out next month when it goes in for the next maintenance. I am really hoping that maybe there is an issue with the A/C compressor or the pressure or something... Otherwise my current solution is I really only use the A/C now if the wife is in the car, or I am on the highway.
I will update if they find anything out of the ordinary. I would figure there would be more complaints if it was like this for everyone. Otherwise if this sounds normal to you guys, what are your tips to smooth out your driving with the A/C on with the MT?
Thanks!