Fun With Windows

One of our next big tasks for the house is to clean up the glorious original windows. We priced out replacements, and our options were: 1) order high-cost custom replacements, or 2) reduce the size of the openings so that standard windows would fit. Needless to say, neither seemed a very good option. So instead, we decided to remove, strip, and recondition each of the windows in the house, one at a time.
Now, for any of your who haven't ever had the pleasure of stripping paint, it's, well, not a very pleasant experience to say the least. The fumes alone from most paint strippers could kill an ox, and if you happen to get any of the stuff on your skin, it feels like that time in chem class when you spilled the "Caution: Do Not Spill" bottle on your hand. To top it off, most are highly toxic to the environment.
So, being the eco-conscious citizens we are, we set out to find a eco-friendly stripper that wouldn't singlehandedly change our yard into a Superfund site, but would still take off 116 years worth of paint and crud. Enter Ready-Strip.
This stuff promises all of the above. I have to say I'm a bit skeptical, since it's one of those products you see on midday infomercials, but all the reviews seems pretty positive. So, we headed down to the local paint store and bought a nice big bucket of it.
Right out of the gate, I can tell you that it smells just about as strongly as the normal version. Albeit, its odor is a bit more pleasant; I would describe it as strong blue cheese (yeah, call me crazy, my wife did until she smelled it too). Its consistency would best be described as, well, like snot. It's goopy and gloppy, and if it wasn't meant to remove paint, I'd almost say it would make a good stand-in for the above-mentioned bodily fluid.
The directions say to leave it on until it turns a pale green / white, then to scrape off the paint with special scraping tools designed for this purpose. Our plan is to get the windows as clean as possible, then re-paint them a nice off-white to match the rest of the trim. One window already will need some more structural work, including re-gluing the bottom rail (I think that's what it's called), and of course we'll re-glaze the lot as well.
Now comes the tricky part... in order to get the windows out, we had to remove the two "stops" holding them in on the window frame. Seems like an easy task, no? Well in this case, it turned out to be a bit more interesting. Whether it was years of paint, or some other mysterious cause, they proved a real bear to remove. In the process, we seem to have uncovered a bit more work to do!
Help Us!
As you can see, our frames look a bit worse for the wear. It turns out they've been pieced together from several different chunks of wood, seemingly without any particular plan. The question now becomes: how do we fix it?
So, fellow bloggers, we turn to you for advice. We've already read several books on the subject, however we'd love to get some practical advice from anyone who has already taken on this task before we dive in. Do we rip out the whole thing and frame it from scratch? Or can we just patch the damaged sections?
Luckily, we have storm windows, so they can provide at least some protection from the elements while we're completing the work. Still, I heard somewhere that storm windows aren't too good all by themselves. Kind of like lime juice, tonic water, and gin... by themselves, not too appetizing. But combine them together, and voila, a nice refreshing G&T. :) Sooo, if anyone has some tips to help us, it would be greatly appreciated! Stay tuned as the saga of the windows continues to unfold.