I backhalf a few jeeps every year for other people and I can tell you this. Once the rig is done, they ALL say they wish they would have nust went full tube buggy due to the amount of compromise needed when working with a portion of the factory frame and tub. Best advise I can give is keep the outer shell of the YJ tub, and build a full tube chassis for it to sit on. That is what I did with the buggy below. Its a full tube chassis, but I built it in a manor to allow a scramber shell to sit on it. Factory windshield, doors and soft top all fit.
I doubt it is.. It started out as a stock YJ that was then built with a 4 link and tons sourced from me. The owner then decided to backhalf the jeep
He then came to me wanting help with a sbc swap he was doing, and while the jeep was at my shop things got a little out of hand, and the majority of the tube work he did, as well as the front half of the frame were cut off. The jeep lost 6" of ride height in the process. Below is a link to the entire build http://www.misfitjeepers.com/viewtopic.php?f=8&t=73
This is the inspiration I'm planning to use when I do mine. Really only keeping the firewall and the floor if my plans go as expected. I understand the thought on building a chassis instead of tubing the jeep, but I have everything setup the way I like so not worried to much about any limitations. I'll go a bit higher on my rockers than this link did, and not keeping a windshield, but I like the lines.