Have you tried the "flip" stop technique? It prevents a lot of that.
I've never tried the "Flip Stop" technique. Interesting. Looks like it works pretty well. ...my method is certainly messier than the flip stop. I'll try flipping it next time I use the stove.
It works very well, but it doesn't have nearly the same potential for warming up your arm that your method has.

As for flare-ups: This is the biggest problem with liquid fuel MSR stoves. It is hard to tell people how to do it, but I have never had any trouble. Simple instructions:
Open. Close. Light. Wait until flame almost goes out. Then open the second time.
Yep, that's about right. You can also use alcohol. I use alcohol in a squeeze bottle. With the squeeze bottle, it's easier to control the amount dispensed, and you don't get nearly as much soot with alcohol primes.
HJ