-Why are my upload speeds a fraction of my download? 12mbps on a 400 down plan.
The current upstream / return path bandwidth spectrum allocation on DOCSIS is physically limited. It's the nature of the beast. This why there isn't as much flexibility with offering faster upload speeds compared to the download.
-Why is my tested download speed not up to par with my maximum speed? ~250mbps on a 400mbps plan.
Call 1-800-comcast and ask a rep to completely remove the modem from your account and to "re-provision" it from scratch. Also ask them to confirm that the provisioning and account data in their database is correct and complete and that the correct configuration / bootfile for your subscribed to speed tier is being pushed to the modem.
-Why is a plan with such high speeds offered in an apartment far from any server and one which still uses cat5e cables?
Don't understand this question. Please clarify.
Comcast does not do the wallfishing of cables anymore. You'll need to hire a low voltage electrician for that.