The issue with transportation is due to the road closures. Especially for the full marathon, roads are closed all over property until the runners are done on them. For instance, the stretch of World Drive that goes under the lagoon, and runs between the Contemporary and the MK bus stop, becomes a single lane for a stretch. So traffic gets stopped on both ends, and then they let it through in a single direction for a while, and then switch. If you are staying at the GF I would strongly suggest using the Monorail to MK and Epcot in the AM each day as that will let you miss most of the problems. Then transferring later on once the roads are open.
The routes are actually fairly easy. For the half on Saturday, the runners only do MK and Epcot. And MK is pretty much clear by the time the park actually opens for the day. For the full on Sunday, the same applies for MK, but runners will be in AK and DHS and Epcot while the parks are open, in that order. But many of the runners are there for the race, and not the parks, so if anything the hotels and restaurants outside of the parks will be busy, but the parks shouldn't be that bad.
Since you are planning on being at Uni on Sunday, that will be the toughest part for you. The running route uses the main road by the GF (exits out the back of MK and then meanders to AK) so the only way for you to get to Uni may be blocked, or seriously restricted. I would suggest on leaving extra early just in case if you want to get to Uni for rope drop.