We are not expanding our home at all, just putting a kitchen into what used to be the garage, laying flooring, and separating the gas/electric.Does anyone have any thoughts on what we should expect to pay a contractor to this work in Sonoma County?

Some regulations exclude this arrangement from the codes when the owner is sharing kitchen, bath with roomers.The plus to that is if they cause problems you do not have to evict you can simply put their property on the curb and lock them out without notice.

Only entrance after this was through a pass through bath from the kitchen!

But that was the best thing that happened to me personally because it forced me into heavy research and to see Real Estate for what it was becoming and was PROBABLY going to be (IE: doing the prep work in the kitchen before cooking a meal) as opposed to what it was (IE: a delicious dinner already cooked and ready to eat).Being forced out of our preferred market is what put us on our current multi unit adventure.  

I have a unit to renovate in boston and wanted to know labor cost (including only rough materials typically supplied by the contractor) of1) a averaged sized kitchen remodel (i.e.

It's a huge kitchen and worried it won't come out well.

On specific deals you can get actual numbers for insurance, taxes, and do better at guessing maintenance based off of how old the systems are and how much square footage of carpet, paint, how big the kitchen is for when it needs new cabinets etc. 

I have budgeted for the reno accordingly, but my only concern is the kitchen.  

Additionally, let's assume the property is fully rehabbed (3 units, now worth 1M) - gutted to the studs, new electric, new plumbing, new walls, new kitchens / baths... etc... would you still apply the same % or calculation on how much to set aside each month?

I bought a 2 unit, and I would've had them check the popcorn ceiling in the kitchen for asbestos.