We are about to have a major redo of our roof / attic, where 2 layers of 3" foil-faced polyiso boards will be installed taped and edge-foamed.
The layers go like that (from bottom up):

Drywall
Framing (of attic floor)
Plywood
First Layer of Polyiso (glued) to plywood, seams taped
Second Layer of Polyiso (glued to first, seams taped)
attic space
Roof framing
ZIp roofing (OSB type material)
Ice and Water Shield (valleys and bottom 4 ft of the roof)
Shingles
 
The roof will have continuos soffit and ridge venting. The overhang is 2 ft wide.  We will puncture little holes in the foil of polyiso boards to somewhat eliminate vapor barrier (as was recommended on this board).

It is somewhat strange situation in a sense that attic floor is pitched (at around 2/12), because it is actually the decking of old roof (we are building a higher pitched 6/12 roof over the old roof while insulating at the same time on the plane of the old roof). I know it soounds strange.

My areas of concern are as follows:
1. 2 ft wide Soffit is specified as rough-sawn plywood. With the top surface of polyiso potentially acting as condensation surface and dropplets of water going down (at 2/12 slope) most of this moisture will end up in the soffit. Is rough-sawn 3/8 fir plywood (will be primed from all sides) be appropriate for this ?

2. Do I need to get tar paper installed between the plywood floor (old roof decking) and bottom layer of polyiso ?

3. Any other ideas / recommendations / criticism ?

Thanks in advance.

There's no point perforating the foil facers to reduce vapor retardency in this application. The only time you'd want to do that is for below-grade foundation walls in order to let foundation dry rather than saturate and cause the sills to rot. Otherwise, since all of the insulation is going to be iso, high-retardency facers are the way to go.

Sealing the ends of the iso with spray polyurethane at the soffits will minimize seasonal uptake of humidity into the iso, but even that is probably overkill.

There's no point to tarpaper between the iso and the plywood floor and gluing it to the roof deck might be contra-indicated. Look at the iso manufacturer's specs for mounting it on roof decks- some sort of slip-surface material is often recommended. But since this won't be subjected to direct sunlight the delta-Ts will be far lower, so the expansion/contraction issues are likely to be less than half that of a flat-roof hot-climate torch down application.

R36-R40 isn't a huge amount of attic insulation for heating dominated climates- what is your location?

Blowing 6-9" of low density cellulose would be pretty cheap- a lot cheaper than another 3" of iso and would be the equivalent of adding another lift of iso. Depending on your climate and the depth of the joist (former-rafter) cavities it might be both cheaper & better to go with a full cavity-fill of cellulose and only one layer of iso. A 2x10" framing cavity runs ~R30+ with 2lb cellulose, over which you'd be adding R18+ of iso for a total in the neighborhood of R50 instead of R40, all for less money.

Also, since you're not exactly space-limited up there, it's generally cheaper per unit R to go with EPS. It would take 9" of EPS to be roughly equivalent to 6" of iso, but the cost would likely be lower. It's vapor retardency at 9" would also be reasonably good, but not as restrictive as four foil facers in the stackup.

The only time you'd end up with condensation running down the iso in a ventilated attic would be if the attic temp were dramatically lower than the outdoor temp in the humid summer- which would be nearly never. Painting the interior of the soffits won't hurt, but isn't necessary. Were the roof were to leak you could have water running down the iso though, but presumably that would be detected & corrected before months/years went by.

DANA1, thank you for your comprehensive response.

To answer some of your follow-up questions: This is in Chicagoland.  Making holes in polyiso was intended for a case of an occasional unforeseen leak (in addition to any kind of condensation scenario) - to allow moisture to dry inside (or outside). I would be glad not to make any perforations (it is more work and "less" insulation), if you don't think it would be beneficial. I thought of doing it mostly because the new attic will be very small and it will be very difficult / expensive to change the future setup once everything is in place (in case of mold / other moisture related issues). I was also thinking that a glue (if used) would better adhere to polyiso foam (in the areas that were punctured) than to aluminum.

In terms of cost savings, I already have the polyiso product, and the cost was very attractive ("insulation factory seconds") - thank you and other at this forum pointing me to these great people with nice product.  My 6" will run about $1 per sq. ft. in material (not yet including glue, tape, etc.) This is essentially a "wall" polyiso product, but I will use it in the roof / attic application. Also, at the top plate (and close by) the height is limited, I will have about 8 inches total and will need 2" for venting (I don't need baffles in this case, correct ?).

How would you "detail" polyiso in this new "attic" around the chimney (I have two that need to be done) ?

IIRC 3" clearances from chimneys & flues to the iso would be required. (Standard clearance from combustibles.) In a non-accessible attic with no ducts or vents connecting it to conditioned space nothing else would be required.

Baffles are only required for fiber insulation to keep the insulation from shifting in such way as to block the venting. They serve no purpose with rigid foam.

Construction adhesive works fine with aluminum facers- you'll probably be just fine with a glue-down only, but seal the edges with spray foam if you can.