i have recently used one of the Onboard Vintage Tube Screamer Booster things from axes r us. I had my cousins old N3 here (as well as a lefty N2 for a new neck). These things have huge control cavities but only knob so they are perfect for adding new stuff. Anyway my cousins N3 now has the VTC and a vitamin Q capacitor on the tone control. The VTC is very harsh if left on full but good sounds can be got with a little tweaking and carefull use of the tone control to mellow out the spikes. It certainly adds a very usable element to the guitar.
The guy who is having anew neck on his N2 saw it and now wants stuff adding to his as well

I also have one of the MODboard delay circuits sitting around here. Guitarfetish deliver to the Uk. Havnt gotten around to using it yet so cant say how it sounds
TBH i never think on board effects are a good idea but always end up buying them on a whim.
The modboard and axesrus stuff both fit easily into a guitar without much modification - to get the guts of a pedal in there you may have to do a bit more work.
getting a BYOC kit and hooking it up will certainly be the best option as far as sound quality is concerned - and shouldnt be that hard to connect up either.. but you need to think about a off/on switch rather than the stomp switch
give hooglebug a message as i am fairly sure he has done the fuzz factory thing like matt belamy on his mirror top guitar:
http://www.myspace.com/afguitars