Hey guys, as a quick update I wanted to let anyone who was curious know that I ended up fixing the issue I posted in this thread: http://goedhartvoordieren.nl/?page=r/ccna/comments/8jdqzt/cisco_lab_issue_2811_routers/
I took everyones advice and started from scratch and checking every single variable I could. I even downgraded two of my routers to 12.4 to see how that interacts, when I noticed that port 0/0 stopped communicating with other 0/0s, which wasn't a problem until now. One of the things that a lot of people were suggesting was using a crossover cable, but I was using one and it didn't work. But the crossover cable worked when trunking my switches, so I automatically assumed the cable was good (I made the cable myself). I work for an MSP (different division than me, but I know some guys there) and talked to a couple of cisco guys. I explained the whole situation to him, and he was very adamant that there is something wrong with the crossover cable. At this point the only thing that made sense was that auto-MDIX was screwed up. I checked my cross over cable and found the 2/6 pair wasn't done correctly. I fixed the cable and tested, and the routers work perfectly!
What's bizarre though;
I set R1 and R4 to 15.1. R2 and R3 are 12.4. Neither Port 0/0 or 0/1 of R2 and R3 have auto-MDIX. R1 and R4 have auto-MDIX, but only on port 0/0. I don't know why they couldn't put that feature on port 0/1, but there you go. I'm going to upgrade R2 and R3 back to 15.1, make a couple more crossover cables and forget that I spent 10 hours troubleshooting what ended up being a cable issue. And my ignorance, since I should have listened to everyone sooner.
Hopefully this explanation will help others in a similar position in the future. Googling didn't really help me, but maybe this will pop up on Google for others.