You'll need two things:
BrawlBox (v0.73b is newest)
An untouched copy of the original PM 3.5
Your modded copy of PM 3.5
In BrawlBox, open the stage .pac file you need from "projectm > pf > stage > melee" from the untouched copy of PM 3.5.
"Right-click > Extract" the following files from each stage file you need. There may be more than one of each of the following (e.g. Dreamland has multiple cameras) or they may be under slightly different names, but in those cases just extract all of them and ignore the minor name differences. #'s and X's represent some parts of the names that I at least think vary in most cases. As your extracting these files, you might want to save and organize them for each stage in case you need to repeat this process again later. Under "ARC 2" you should find and extract:
* ModelData[100] > 3DModels(####) > stagePosition
* STPM
* SceneData[0] > AnmScn (####) > StgXXXX > Cameras(####) > camera0
Now, still using BrawlBox (you don't need to save anything), open "projectm > pf > stage > melee" again, but for your modded version of PM 3.5 instead. Open the modded stage .pac files, and go to stagePosition, STPM, and camera0. "Right-click > Replace", and then replace them with the files you extracted. This will give them PM 3.5's stage boundaries and cameras.
For some stages with platform functions, stage hazards, or just different stage/platform shapes and layouts, this won't work (excepting cameras, which probably wouldn't be affected unless the stage sizes are absurdly larger/smaller than the originals). Dreamland and Distant Planet "shapes" won't match previous 3.02 and older PM versions of those stages, but the differences are minor if you're not using this for tournaments. Yoshi's Island ghost platform timings will be different, but the "shapes" are the same. Other than those exceptions, you should be set (at least with the tourney official ones; idk about others).
