I have a older 2 story flat roof building in NYC area and i’m looking to do renovations. IT use to be some sort of machine shop a while ago before most of the windows were sealed up.

Now i’m looking to renovate and get windows installed again.

The original windows were double hung with weights, single pane glass which was unfortunately broken so plywood could be put put there. The original window frames are in various states of decay so I removed them down to the frame which is 42×80

My main question is when looking to flash the window, but first i’ll explain the construction type.

From inside out,
1) 2×4 frame (balloon?) brick filled. Wha would be a header in normal construction is wood that is mortered to brick. I assume it was part of the old window framing. 
2) Diagonal tongue/groove 1×4 boards (sheathing?)
3) What I assume to be the original siding, horizontal wood that isn’t flat, can only describe as like a wave. 
4) vinyl siding. 

Looking for best practices here on how to flash the sill. Here were my 2 thoughts
1) suresill/jamsill? Then flash the sides with tape.
2) flexwrap the bottom with a sloped sill using cedar siding nailed to the original sill. Then tape sides.

Then how to flash the head 
1) peel back wood siding and install z flashing?
2) Can i just flexwrap on the diagonal sheathing if I peel back the horizontal siding?

I think the original window external trim is still on the outside, I’ll get some pictures when I take of the vinyl siding 

I also attached a separate pic of another window but the same construction type.

My 2nd question is since the rough openings are quite large, windows in that size are more than what I was budgeting. If I reduce to what I assume to be a common size, 36×72, I can get pella fiberglass for 800 vs 1500 for the larger size. If I do decide to get a common size, would I just block using 2×4? Or is there a better practice.