How to decode a caesar that goes to transposed plaintext? When decoding vigeneres, I am left with Caesars. Often when the key is longer, these are shorter so normal frequency analysis won't work.

Is there another method I can implement without adding a load of loops?
The most frequent letter will probably still be e or t, this uniquely determines the ceasar shift, this leaves maybe a few options. You can also do a $\chi^2$ test to match the alphabet in the subcipher with the standard one, or use bigram frequencies to rate combine shifts in adjacent alphabets.

If all alphabets are mixed, not shifted standard alphabets, it's quite a different story, and will depend on the exact method of keying and square construction.