Here's my thought on a "new" frame which would actually make this a much more bite- sized and manageable project and better suited to what you're describing:
You get the used frame, clean it up, repair it where needed, prep it, paint it and then that's done. Meanwhile, you look for a set of wide track axles which you rebuild at your own pace. Once they are completed, you get a set of YJ springs and now you've got a rolling chassis. Put it in the shed.
Now you look for a 4 litre on Craigslist with a 5 speed, order a clocking ring from Novak and get a cheap, used Dana 300 to rebuild behind the 4 litre's AX15. You might even sell the TJ transfer case for what will pay for the 300. You can drop the 4 litre on to your rolling chassis and now it's the prefect workbench for new gaskets, seals, etc. on the engine and 5 speed.
Get a 15 or 20 gallon tank out of Craigslist or a wreckers and run all your fuel lines from the donor 4 litre as well as an in-tank pump. Order all your brake lines from inline tube and run those easily and safely while it's a rolling chassis.
At this point, your rolling chassis is done and is a dependable drivetrain. Now you can pull the body off the old scrambler and focus only on rust repair. New/replacement panels where necessary, sheet metal patches, liberal use of spray-in liner and paint and you're ready to make a Scrambler again.
Painless Wiring harness or very careful restoration of your original harness and it's simply a matter of putting a puzzle back together with cleane/repaired parts.
I know this sounds slightly overwhelming but it really isn't. It can be done in bite- size projects, whereas repairing the current frame really cannot. I've done almost exactly this project myself in the past and once you get started you'll be amazed how quickly these things come together.
When is done, you'll have a very safe, reliable and fun driver which will never lose value. You'll also be able to sell a lot your old parts on Craigslist for more than you think you will.
Just some thoughts.
