First of all, thanks very much to everyone who answered, that's what I love about this forum.
Special thanks to @Woland for your long and specific answer.
I've been doing some testing on these things, I post what I found in case somebody else finds it useful:
- The error in 2.6.1 was indeed caused by my 3D models, but not by the file itself, rather than the path. For some reason, if I put the 3D files in my desktop, Isadora has no trouble, but whenever the files are inside any folder, the error window pops up.
- The mouse watcher error only happens with an imported 2.6.1 patch. The mouse watcher works as expected in Izzy 3 if you make a new patch, but it doesn't if you open an old file. Maybe if I was able to save it (updating it in the process) it would behave correctly afterwards, but I have no way of knowing this... yet.
- As for the Blur taking up a lot of CPU usage, I found out that a missing FreeFrame plugin could be the actual problem. After I installed the FFMotionBlur (which was in the 32-bit plugins folder but not in the 64-bit one) the scene runs in Izzy 3 more or less the same way than in Izzy 2.
Thanks again everybody. I think I will be updating to Isadora 3 very soon, since it's clearer now than the problems were more closely related to using Izzy 2 in Mojave and I really want to try some of the new features (like Blind Mode and such). Cheers.