What are you hoping to get out of the relationship? Are you looking for them to help you put together a 5-year tech plan or are you just looking to have someone talk you through some specific problems you're having?
It sounds to me like this would be money well spent.....assuming you find the right vendor. It sounds like you have a lot of pieces to this jigsaw puzzle and a fresh set of eyes may help you put them together.
I don't think this is something you'd want to entrust to your local MSP, very few of them offer really good fractional CIO services. That said, there are definitely vendors who specialize in this sort of thing, even ones who specialize in non-profits.
Just make sure that you properly define your scope of work at the beginning. The better the scope of work, the more likely you and the vendor will be happy at the end.
I'm anxious to hear how it turns out. It sounds like a good story for the monthly call.