Hey! Sorry for the big bump, but I heard that you stopped working on this project due to a problem you encountered re-inserting your levels with
Level Tool. I've figured out some important details about the proper usage of that program, and I'll be sharing what I found with you here so that, hopefully, you'll be able to continue making this hack.
In
this comment you mentioned that you could no longer open your ROM in Golden Egg due to a problem with a level header (likely that it's out of range for Golden Egg). This suggests to me that you're working with a headered ROM. The problem is that
Level Tool does not properly support importing level data onto a headered ROM. Importing to a headered ROM will create levels with incorrect pointers (either out of bounds for level data or overwriting important game code) and with very obviously incorrect byte counts. You must either remove the header when prompted to by the program, or use an unheadered ROM when importing your levels (you can re-add the header later, after you import.)
I also noticed that you've encountered some strange bugs in the past after reinserting stages. What's likely happening is that Level Tool has overwritten some sprite/object code with level data. In order to avoid this, make sure that you
press "Clear Levels" on the recipient ROM before you import your custom level data. For whatever reason, not doing this beforehand causes problems.
Hope this helps, and that you're able to move your project over to a new ROM successfully.