I'm inclined to agree that you could reasonably have assumed that GRWBSC would want you to use their technology. At the very least they should have been told up front that you weren't planning to. That would give them the option of changing their requirements to be more specific and you the option of re-estimating the time/cost based on the changed requirements.

If you haven't tried PerlEx from ActiveState, you might be pleasantly surprised how easily you can move your apps from Apache to IIS - I know I was. It's not free but your can try it for free and the retail price is probably less than a few hours of your time.

If your application is dependent on MySQL's dialect of SQL, then you could continue to run that on GRWBSC's operating system - NetCraft won't have any visibility on that.