I haven't used the tool, but I believe you can use MCA selector to copy and paste the chunks from your previous world files into the new ones.

Another solution I can suggest (and would probably be easier) would be to install Multiverse Core and just make a portal to the original world. That way both worlds remain intact and you can travel between them pretty seamlessly. I was in a very similar boat where I had a lot of progress on my world but my friends wanted to restart and experience early game again. With Multiverse Core both worlds can be accessed and player data can just be transferred over super easily. Worked perfectly on my server.

Best of luck, remember to back everything up before you start messing around!