About 6 months ago I got an email from someone making a longer top and his experience may help here. He lengthened his YJ to roughly LJ length (so about 9" shorter than a Scrambler, but the info in this post still applies to lengthening a top for a Scrambler). He cut two YJ hardtops in half and spliced them together into a longer top. A YJ or CJ top would be a reasonable choice to modify for a Scrambler because it fits in all the important places - at the windshield header, around the doors and across the back.
Here's a photo he sent me of the spliced top:
He also sent me this next photo, which shows what happened after he painted the top and then had a glass place cut new longer glass for the sides - I guess neither he nor the glass place realized that the factory windows in those hardtops are curved, so when you make glass for the longer openings it needs to be curved too.
Custom curved glass being out of the question, the reason he sent me the email was to ask what to do about it.
I sent him a long email explaining how to modify the window opening so it would accept flat glass. I told him the steps required to modify the window mounting surface so that it would follow the yellow dashed line in the illustration below. I also sent him several other possibilities he could consider, but modifying the window mounting surface to be flat is the one I thought was the best approach.
I don't know how his project ended up, I sent him the detailed email about 6 months ago and haven't heard back.
One other complication with lengthening factory hardtops, which I've highlighted with the red line in the illustration above, is that the top of the roof is curved from front to back. If all you do is cut and splice two hardtops together, you'll end up with strange humps in the middle unless you do a good deal of bodywork to smooth things out, something that doesn't seem to have been done on the hardtop above. Now that I've pointed out the bulge with the red line, look back to the first photo in this post and the bulge should be obvious. The same would be true if you tried to lengthen an LJ hardtop the 9" necessary to make it fit a Scrambler - lots of bodywork on the roof to make the curves look right.
I'll also comment on the idea of modifying a JK/JKU hardtop to fit a Scrambler - besides the fact that the JK tops are too wide at the tub, there are virtually no straight lines on a JK top - the sides are curved, the back and tailgate are curved, the roof is curved, it's curved at the windshield... to make a JK top fit not only would you have to section it to make it the right length and width, you'd have to change pretty much every curve on it into straight lines. Having just spent a lot of time designing and building a custom JK hardtop I can tell you it is quite challenging to deal with all the curves - for this project it would be a lot easier to start with a CJ/YJ hardtop than a JK hardtop - I think it would be less work to make a completely custom top for the Scrambler than it would be to modify a JK top to fit and look good.
My advice is to start with a YJ or CJ hardtop if you want to work in fiberglass, or start with postal Jeep body parts if you want to work in metal, like this project that apparently never got finished:
https://www.cj-8.com/forum/showthread.php?44713-DJ5x2-Metal-Hard-Top
Whatever route you might take, there's no "quick mod" that makes a hardtop from another model Jeep fit and look right.
Having built custom hardtops for YJ's through JK's, I'm happy to answer any detailed questions you might have about various options for modifying/building hardtops to fit.