Some Update and photos.
I have been working on Fiberglass for the last 2 weeks (on and off) The main thrust has been to cover the trans tunnel and reinforce the seat mounts I installed. I also installed a Ebrake lever mount into the floor, which is requiring more reinforcing.
The reinforcement looks pretty cobby right now but I will sand and fair it in before I'm done. Also the entire area gets covered by Dynamatt and carpet, so strength is more important than cosmetics.
I have also stripped the fiberglass doors, and am proceeding with fixing cracks etc.
One thing I do have to relate to those who are interested is that finially I found the source of the sliding windows, not only for these doors but for just about everything that has a sliding window, IE RV's, Boats, Jeep tops, you name it.
The company's name is Statewide Aluminum. Located in Elkhart IN (big surprise?,RV capitol of the world)
http://statewidealum.com/index.htm 
great people!
This outfit has been making windows for 40 years and in fact they made the ones I have. Unfortunately they won't make just 2 for me as they are no longer a normally produced item . Since the only thing wrong with mine is the weatherstripping they have agreed to supply me with small quantities of the 4 different types so I can replace what I've got., and essentially end up with new windows. (more work !!!)
They would however produce a run of 25 sets of windows for me, so if enough of you guys find fiberglass doors we can replace the windows with brand new. around $200/set.
They are Besttop's source for the sliding windows in their upper half doors and soft upper half doors. Best top was kind enough ( after I talked to the right person) to share the source with me.
On to technical:
I was worried about removing the windows from the doors themselves. They were held in place by a interior Bezel held with sheet metal screws, and some black GOO. I removed the bezel from one window and tried to push it out and it wasn't going anywhere. I'm thinking I'll have to destroy this to get it out, so I backed off and started looking for the window source just in case I ruin one, I can get a new one to replace it.
Well I laid the door on a bench with the window side half off the bench, and a few days later I noticed the window frame hanging below the door. The heat from the garage had released the goo and the window just fell out. Luckily it only fell a couple of inches and was unharmed. The back side of this is the fact that this black Goo is one serious SOB to remove. It is the consistancy of tar, and it not interested in giving up. Scrapping and some expensive guncleaner seem to take it off, but it gets everywhere.
Since new widow assemblys are not available I will have to disassemble them by removing 2 screws and drilling out 4 small pop rivets on each frame. This will allow me to replace the weather stripping, in exactly the same manner as the windows were assembled at the factory. Since the window frames are a little scratched up I'll either have them reanodized, or paint them with the same paint as the upper half of the body.
I'm debating whether or not to remove the lower windows as they will have to be done by pro's. I would like them out so I can deal with any fiberglass issues on the doors better, but it may be a real hassle to get them out of the doors. We'll see.
Talked to the painter Friday and he said he could match any color I choose. I have to paint some of the items that are parts of the body before the body is actually painted. Items like the grill which is a 4 hour job to completely cover with paint and doodads like the door, windshield, hood and tailgate hinges The tailgate and the doors have to be painted before the weatherstripping can be applied, and the Windshield frame itself has to be painted before the glass, the wiper mechinism, and the cowl seal can be installed.
Also I want these items painted with a much stronger paint than is used normally on cars. The paint I'm using as stated in an above post is Cardinal 6400 series Polyurethane industrial paint. The grill will be much more resistant to chipping caused by flying rocks when painted with this stuff. Metal parts will just hold up better. This paint has a slightly lower adhesion number than powder coating, but it is much more flexible so it doesn't chip during impact like powder coating does. I am also painting the entire frame and undercarriage with this paint as well as the bottom of the body and interior of the engine compartment. Chip resistance is the reason for all of this extra work. Corrosion elimination is the reason why I'm painting all of the individual parts of the undercarriage before final assembly.
All of the body parts, IE tub, fenders, hood, top, will be painted with some kind of superduper Dupont car paint that is base coat, clear coat/2 stage. Apparently this stuff drys in like 20 minutes, and then they put the clear on and it drys in 20 minutes too! less time for dust and dirt to attach itself to your paint job.
All of this may seem like a bunch of unnecessary BS to go thru for a Jeep.
I plan on driving this thing for the rest of my life.
Randy