Minor update: After the fiasco I had with my rear caliper, I decided to take my master cylinder apart and rebuild it. As I took it apart I noticed that everything inside was rotted pretty bad, there was even sludge trapped inside there. I also noticed that the pushrod was rusted/rotted and bent bad (previous owner tried fixing this by coating it with shiny paint). After seeing this I decided to play it safe and just get a new setup. I researched and found a couple old posts (some by Hawaiisr, thank you sir!) saying that a 450r master cylinder will fit on a 250r frame and the internals of a z400's master cylinder will work with a 250r's master cylinder. I looked on eBay and discovered that it would be about $10 more for me to buy the z400 and 450r master cylinders than it would to buy a 250r master cylinder in okay shape. I decided to go with the newer setup and bought both. I used the 450r master cylinder, z400 push rod and I cleaned up the clevis from my old master cylinder and threw that on there. I also switched out the inlet for the brake fluid with my old master cylinder. This new setup actually looks pretty snazzy! I just need to route the lines and I'll finally have working brakes!
If anybody has any questions on the setup, or if anybody wants better pictures let me know. I figured I'd post this here in case somebody decides to search for this info in the future.
Here's a pic of it mounted on the frame and a comparison of the old setup with the new one:
