Anytime you run a power adder, be it nitrous (or nos as you call it), a turbo, or supercharger, you are increasing the risk of damage.
A safe tune is only as good as the one doing the tuning.
The risk you take with a manual tranny and nitrous comes when you miss a shift. If you hit the rev limiter, the factory computer will shutoff fuel flow. NOT good when coupled with nitrous.
An RPM window switch, when setup correctly, will shut the supply of nitrous off BEFORE the engine reaches the rev limiter, and in turn keeping the nitrous from being added when there is no fuel with it.
In other words, with a window switch that is working correctly, you can miss shifts all day long on nitrous, and it will do the same thing as when you miss shifts running naturally aspirated.
Back to the orignal topic, I did the AOD-T5 swap a few years back, and am still loving it. After selling my AOD and related parts, and after finding a cheap used T5, I finished the swap being only $150-200 in the hole. Not bad for a half second reduction in ET.
If I were you, I would do the swap and never look back. Just don't let Josh drive the car when you're done
