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.  

Nine windows one is a pretty big window that goes across the living room and two windows have to be brought up above the counter tops as we converted a dining room into a bigger kitchen so they are moving some siding around as well to raise two windows.

If you are looking for an income producing property to add to your portfolio, this one is definitely worth a look.Property features include; Block construction, good rental history, newer tile flooring throughout, updated kitchen cabinets, newer ceiling fans, all kitchen appliances included, no neighbors across the street, sturdy roof, updated landscaping, window AC units, central heat, convenient location to area playground and parksRent Rehab: None expected

Now, if you are in a rental situation where there is continuity between all the rooms already and you are looking for the next level of pizzazz, you can update old laminate counter tops with new laminate counter tops, lay vinyl plank flooring in the kitchen and bath, spend a little more on bath and kitchen light fixtures, add a few USB charging outlets, install ceiling fans in bedrooms instead of flush mount fixtures (but remember, more moving parts means more points of failure which can equal more maintenance calls - however if you are getting better tenants and higher rent, maybe that doesn't matter - I personally try to remove points of failure - spray hose from sink, ice maker from freezer, garbage disposal, really anything having to do with water).

I'm wondering, what should my plans be in terms of figuring out what size to make the rooms, bathroom, kitchen, etc?

We hung 142 sheets of drywall, rewired the entire house (my stepson is an electrician) redid the entire kitchen, and laid 2500 sq. ft. of vinyl laminate flooring among other things.