Anyone ever ran an amide coupling reaction using the TFA salt of the amine?

I recently had a problem with unwanted TFA-amide as a major (1:1) side product when doing EDC couplings with the Amine-TFA salt. Using the freebase worked nicely, but I'm sure HCl salts would be just fine.

Is there a particular reason why tho. Its not like the TFA can't be removed easily with a few washes or rovapping as well.

Yep, do it all the time. I typically use other reagents than carbodiimides such as hctu and bop. But adding some base during the reaction should just work fine.

Yes, I imagine so since TFA salt can be coupled to NHS or HOBT. You should do a basic wash to free your amine and get rid of TFA salt. Be careful though since your free amine may prefer the aqueous layer instead of the organic layer. If that is the case, you should consider using another acid like HCl and then leaving it in salt form. React with TEA, etc to deprotonate.

I have done it many times from TFA salts and you should not have any issues.

I've done this, albeit reacting an NHS-ester with the TFA salt of an amine. I just made sure to add enough excess of a non-nucleophilic base (TEA, DIPEA...) to the amine before adding the NHS. In my hands it worked satisfactorily...