Yeah, I'm with noodles. It's your guitar, if you want to replace the electronics, do it. I'm pretty sure you're a skilled enough tech (or know someone) that you can remove it all carefully and keep it set aside in case you want to restore it to its stock condition for future sales. You just have to decide:
Do you love the feel of this guitar but want different sounds/features out of it?
Do you want to keep it as a unique guitar in your arsenal that has very specific features that you don't have in any other guitar?
Personally, unless you plan on making it a main player due to feel and sound and all it's missing is a good neck pickup tone, I'd keep it the way it is for the times you want the Sustainer and when you're looking for a neck pickup, grab a different guitar.
But then, I'm a guy who has a vastly different guitar for every purpose, rather than a bunch of similar do-it-all guitars.