You're into the realms of "why do people fit complete sides?" The window channels and windows can be removed simply by (a) removing the inner wooden capping on the waist rail (chrome raised head screws and the rear seat backrest brackets and the door stay brackets), (b) sliding the glass out of the vertical slots front & back, (c) pulling the glass gently inwards at the bottom. The old channels will disintegrate nicely. Now you're left with the main wooden waist rail, which is where the fun starts.
Look at any parts catalogue illustration (try
http://www.mgm-spares.co.uk/catalog.asp ... 7336001347) & you'll see that the waist rail uses mortice & tennon joints to connect with the front and rear uprights. Therefore, to replace the rail you have to dissassemble most of the frame. The top rear corner is joined using a metal bracket, the lower wheeel arch is bolted to the rear upright, the bolts concealed by the wing. Sometimes there is a diagonal screw near the rear of the rail going down into the rear post.
So now you've taken off the wing, removed the aluminium panels for which you removed the trim to get to the screws (assuming that you could get the crews out) and probably the seats to get good access. You've got the glass out already. You try to split the existing joints without damaging the remaining wood - some of which will almost certainly have got rot in it if the waist rail is as bad as you imply. You now clean up what you can, and fit the new rail. After putting everything back together CONGRATULATIONS: you have one shiny new piece of wood in a tired and slightly rotton surround, and you've spent ages doing the job. Apart from the fiddling with guttering & tacks, it's far better to just bite the bullet and replace the entire side. (IMHO). Good luck anyway.
PS it's quite feasible to trim off some of the joint on the new rail and hammer it into place. Just remember that it is supposed to be structural, not cosmetic.
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