So I've been tampering with the Base.rte/Missions.rte files, messing around with mods and what-not.

I was wondering if it was a good idea if there was a permanent post for a backup file of Base.rte.

If that's not possible, can someone please send me a copy of their base.rte and mission.rte files?

Why not just use the installer file? Far faster than downloading the whole thing over again.
For maximum convenience, install to a different location than your actual game, name the folder "Cortex Backup bX", with the X being the version. Voila, instant offline backup.