I've been reading here while and pondering this but can't decide on the best option, but I'm starting next week so time for critics.

 I have a '55 Cape Cod near Baltimore MD, that has a 420sq foot addition on the south side that is 12' 2x6 for the rafters set to a 3/12 pitch, drywall on the bottom, plywood on the top and the one spot I opened has r11 fiberglass. I'm replacing the whole roof and all sheathing on the 3/12 as there are several soft spots mostly above lights (no surprise).  I'd like to insulate it and am leaning towards EPS foam. The cost and timing issues prevent spray foam. I found a foam supplier and can get custom thickness EPS. I'm thinking cut and cobble in the bays with 2  2" layers with offset seams. My big concern is trapped moisture condensing under the roof deck. There is no soffit vent but  the eve details look the same as the north side which does have soffit venting so it could be added. At present it does not have a vent exit but I'm 90% sure I can vent it into the area behind the knee wall and then it would vent to the ridge vent but that would be best added during the reroof. I plan on air sealing the ceiling penetrations while its open: So here are the main options in my head, in order of preference
1)  4" foam between the rafters and no ventilation (Could probably be added latter if needed)
2)  4" foam between the rafters and put in ventilation
3)   stuff the bay with 5.5" of foam leaving no ventilation
4)   needed repairs and put the rest back together
5)   fiberglass bats and vent channels and put in ventilation
6)  above the sheathing foam, best option Lots of ups but cost, time and permit issues seem unreachable right now.

I'm planning to add intake air behind the knee wall area because I saw 110 degree temps in the upstairs room at 80 degree temps downstairs temps.

I have a lot of other thoughts on this but that's plenty for now.

I tried cobbling foam into rafter bays with lots of caulk and spray foam to seal the cracks; then took some down to check the sheathing a few years later. Roof sheathing was soaked, so I removed the insulation, let it dry then filled the bays with closed cell spray foam.
You will never know if the cobbling worked without checking, so you are better off filling the bay with Roxul batts and adding a vent. Roxul has the same R value as EPS and will be easier to install.
Then, when you re-roof (this year?) you can add foam above the sheathing to get the proper R value.

I'm wanting to do this as I reroof basically, install all from the top, the drywall has a custom finish the wife wants to keep it. I thought about putting a vapor retarder in also but that seems troublesome going from the top.

So would installing 3 or 4" of EPS then covering with closed cell foam as a vapor barrier be a safer option?

The better bet would be 2" of closed cell foam on the underside of the roof deck + R15 rock wool batts. At 2" the foam is sufficiently low permeance to protect the roof deck from wintertime moisture drives, but sufficiently vapor open that the roof deck can dry, and with a ~45% ratio of foam-R to total R has huge dew point margin at the foam/fiber boundary for your climate zone (30% would still work) - it will not accumulate moisture in the fiber. You'd have a center-cavity R in the ~R28 range.

Then when it's time to re-roof you could add layer of 3.5" polyiso nailbase panels above the roof deck to bring it fully up to code.

If timing the contractor an issue the foam could be a DIY using a couple of 600 board foot foam kits (Tiger Foam, Fomo-Foam etc. ) With extra tips and protective clothing etc you'd be looking at ~$1300-1500 for the foam job, which may be more expensive than having a pro do it, but it would be quicker and more reliable than EPS.

If you're doing it concurrent with re-roofing, put R23 rock wool between the rafters and 4-4.5" nailbase polyiso layer above the structural roof deck. It could be just shy of code-min on a center-cavity R value basis, but by having the thermal break over the rafters it'll still meet code on a U-factor basis. eg:

https://www.hunterpanels.com/product-documents/hpanels/speciality-products/108-h-shield-nb/file

If you wanted to take to the full R49 you'd put down a 2" layer of polyiso first, covered by a 3" nailbase panel.

Good article at greenbuildingadvisor which echoes Dana's sentiments on your zone 4A roof stackup. It might suggest a ventilation space between rigid foam and roof deck for ice dam control is advisable.
http://www.greenbuildingadvisor.com/articles/dept/musings/how-install-rigid-foam-top-roof-sheathing