My philosophy? Measure 20 times, cut only  once. Once the  teak was removed(decided to go without teak) the framing and ply overlay was clear. I can easily say that I've spend a week sitting in the cocpit in this condition thinking, calculating and trying to envision the rest of the process. Once the diagram was complete, I was ready for the demolition.
The stringer is your frame base.  Notice the three main frames that make up the foundation of the puzzle.  The first is against the cabin, the second right under the scuppers and the third on the fore side and under the steering box.I drew a diagram of the whole cockpit area and took very accurate measurements for the 50th time.  Take as many photos as possible before demolition starts,  you'll need references.
Tip: a very long 'level' is a must. When you're done measuring,  everything is logged in the diagram and you're ready to start ripping things off....stop and check your measurements one more time.

    The Black Hole

  Very carefull at this point. Two weeks later after every single frame was measured and then ripped apart, there is no going back. The biggest problem at this point is keeping yourself from rolling into the black abyss of the bilges. Now you get a better view of the Perkins (for work), the steering column, the chainplate mount on the stringers, the insulation for the ice box and the electrical panel. Good time to put a couple of coats of paint on the inside of the hull.
Tip: On either side of the hull you'll notice three points where there used to be framing on top of the fuel tank. Connecting those three points by a single frame you create the floor framing for your cockpit well. The cockpit well floor should drain fore (into the already there throughhulls).

  Honduras Mahogany (The frames)

  Calculating the amount of lumber needed is a task in it self.  Researching the issue, I found out that the best lumber to use would be Honduras mahogany, for several reasons. First is alot more rot resistant than Phillipine mahogany and second is strong enough but not as dense as white oak. White oak I was afraid, would not have the flexibility needed for such applications. You DO need some kind of flexibility. My father-in-law's garage became my workshop. 2.5" x 2.5" for most of the frames, except at the fore side of the cockpit well which I doubled.
Tip: if you mount your frames on the stringer (you should) you'll  automatically make your cockpit drain at the right locations (cockpit well and scuppers). Your main frame should fall right under the scuppers.

  Frame assembly

Putting the puzzle together piece by piece. Dry-fit the framing but do not install yet. This will give you the option to calculate routing and flush-fitting. DO NOT forget the massive piece of white oak that makes the support for the mizzen mast step. Route the framing and install flush with the rest of the frames. When you're all ready to 'create' then start by through-bolting the main frames to the stringer (under scuppers,  steering box and against the cabin bulkhead). The cabin bulkhead frame will be through bolted to another frame on the inside of the cabin, thus sandwiching the cabin bulkhead in the middle (look for the belowdecks frame in the galley photo, about 8" above the countertop).  The rest falls in place.  I used epoxy only for the hatch opening's assembly and such. After the whole puzzle is in place, I coated the mahogany with a couple of coats of epoxy.
Tip: DO NOT install ANYTHING permanently. Some day you'll have to take it apart. Route the drains for the hatch seats in a way so that they drain inboard (towards the cockpit well).

    Marine grade plywood   Marine ply was delivered. Three 4x8 sheets of 1" ply. Before you install the plywood, walk on the frames and feel if any given parts of it, feel that they are flexing too much (longer spans). Add sister-frames to them. I installed the ply in 5 pieces. 1) the fore part of the cockpit, stopping in the middle of the main frames (scupper to scupper). 2)the port side hatch area up to the steering box frame 3) from there to the middle of the steering box's back side 4) from there to the steering box's frame on the stbd side 5) from there to the main frame, taking care of the stbd hatch.

      Fiberglassing

 There are no pics of this process since my hands were too sticky with the epoxy to take any.  WEST SYSTEM has a guide to epoxy, found at all West Marine stores. It's fool proof. 'I' did  it.

    Finishing the cockpit.  

Once the fiberglassing is over and a couple of coats of polyurethane paint  were brushed on (mixed with non-skid compound), it's time to start installing various things that belong in the cockpit. Hardware, propane locker, mizzen mast step ( you should already have the new one made),  mizzensheets blocks, cleats, winches, hatch covers and their hinges etc. etc.    The compass binnacle must be wedged from below (fore part) in order to be in a vertical alignment. Remember the cockpit well floor has a fore 'lean'.   The worm gear support brackets were through bolted on to the ply. I used the original hatches since they were in good shape and the teak on them would brake up the monotony of the glassed cockpit. This process is the result of the post- cockpit rebuilt planning I was refering to earlier.  Results can be very rewarding.  Would I do this again?  Hell no!!!  Well...maybe on a Mariner 40!!!