I have all the 1.7.10-4.5.3.54 Project Red Mods installed, the newest MrTJPCore-1.7.10-1.0.2.4-universal.jar, CodeChickenLib-1.7.10-1.1.1.106-universal.jar, and everytime I boot my server it tells me I have missing mods. If I remove all the ProjectRed Mods the server boots up fine. I am unsure what would be the cause of this.

Any ideas?

It would be useful if you could provide the latest log.
But first, check you have Forge Multipart.

Though multipart would be downloaded automatically, I manually placed it in and it worked thank you.