I don't see a problem with a per project pricing, but there are some guidelines to follow. First of all, base your work in days, not hours. Maybe a half day rate if it's in the "office" and somebody else is loading it. In the greater NY area the rate is around 900\Day for field time, just to give you an idea. Make sure that you develop a quotation that has a scope of work, so that you don't get sucked into the giant void of undocumented change orders. This gives you the ability to always explain that the new update wasn't part of the job, and you must be paid for the change (just as the integrator is getting a change order for the new equipment\labor ;) ).

Hope this helps, too.
-Jon