Small update, I just hit a bit of a breakthrough. Turns out MAL has its own internal ID system for their xml files and only use AnimeDB ids for AnimeDB format xml files. Unfortunately as far I can tell MAL doesn't have their id list for download. so now I'm scraping the MAL ids. From what it looks like, this might also fix the other errors I was coming across. I should be able to have everything up and running by tonight or tomorrow.
Edit: Definitely tomorrow, assuming MAL doesn't ip block me for making too many requests. It's taken 3 hours to get 15000 anime id's and I set the upper bound to 100000, so basically it'll need about 17 more hours to finish scraping everything.
Edit 2: MAL cut me off at 16117, but hasn't completely blocked me, luckily my script saved all of its work so I don't have to start over.
Edit 3: Now I've run into an odd error. I can import my list, get MAL to like my list, have MAL confirm what I added to my list, but then when I go to my list it is empty. On my MAL profile it's showing random anime and total time (which is wrong), but the list remains empty. So close yet so, so far.
Edit 4: I can export my imported list as XML, which is a good sign, but nothing actually shows up under My List on MAL.
Edit 5: It works! Turns out my list wasn't setting properly. I should have everything up and running in a few hours.