Regarding the HP and EXP bars being blue, I recolored the UI aquamarine in a recent reupload.
I've gotten the "The script is taking too long to load" at random points in various fangames including Spork, but usually the game works fine after closing and opening again. I thought the issue with your save might've been one that was fixed in the latest re-upload, but this sounds different (especially considering you're using the latest re-upload now). Unfortunately, I don't know why the script sometimes takes too long to load in fangames, and since it still happens when you load your save, it sounds like your file is corrupted.
The only solution I can think of is starting a new file with all of your data you had before. How that would work is you telling me your team (including any PC Pokemon you want to keep) and movesets, items, how far you were, and any other info you remember. Based off that information I'd input it into a new file and play up to the point you got to before so that you wouldn't have to start over from the beginning.