Framing Errors are quite different than clock slips (controlled slip seconds). If you are taking framing errors without controlled slip seconds, then it is simply a bad signal, with errors. If clock slips are frequent and bad enough, they can cause framing errors as well, but it doesn't sound like what you are describing is simply clock slips. If your CSS errors and Framing errors are both incrementing together, then it may be from clock slips.
You may need to look at the line build out of the microwave equipment as the signal may be weak, or even too strong and causing errors.
In this type of setup, typically one TSU will be set to INTERNAL timing and the other will be set to take timing from the T1 port.