The problem will come when you want to change the status of the house to sell it.
If you want to sell it as a single family home (more valuable) you'll need to get the certificate of occupancy changed.
If you want to live in it as a single-family but resell as a multifamily, your buyer will wonder what you've done with the two extra kitchens, and will ask that you reinstall them before he/she buys.
author, "Diary of a Real Estate Rookie"
Insider Real Estate Tips with a Twist of Humor: http://tinyurl.com/2ag28z
This is a much better route than what could happen if you don't: Your neighbor gets annoyed with all the hammering, calls the code dept. on you, and you get a huge investigation fee on top of the original permit cost you should have paid to begin with! Good luck with your remodeling plans, sounds interesting!
Broker, CRS, GRI, ePro
Raving Real Estate
Laramie, WY 82070