No need to get testy. I was curious as to the engine type because most .21 engines do not require cutting. El Pirata dropped a .21BB (from a Savage) right into his .21 Conversion. As far as I know he didn't cut it.
If you absolutely need to cut the shaft, the best tool for the job is the dremel tool already mentioned. To prevent any of the filings, shavings, or cuttings from entering the carb, place the engine in side of a baggy. Poke the shaft through the baggy, then cut it. Make sure you have marked the length you need properly so you do not take too much. Otherwise you will have to buy a new shaft (not cheap).
The only reason I asked the questions I did, was to try and save you some time and money (in the case that cutting didn't go well). If the engine wasn't the issue and something with the conversion or the engine mounting was the problem, then cutting the shaft wouldn't have been the best solution. That is all. Good luck with the new engine.