[PJ352]

I'm planning to upgrade a Spec Roubaix triple to Ultegra derailleurs front/back.

Should I be using a long or short cage rear? Why would I select one versus the other?

Thanks

If you're staying with the triple crankset and just changing f/r der. you'd stay with the OEM (long cage) RD.

FWIW, unless there's a reason to take the opportunity to upgrade, IMO it's not necessary, because you'll see no difference in performance with this change.

Short or long cage RD's are chosen based on total tooth capacity of the drivetrain.
Example: 5700-GS RD total capacity = 39T, 5700-SS RD = 33T

 

[PJ352]

Its more about the positive locking adjustment screws than performance.

YMMV, but I've used both 105 and Ultegra and never noticed any difference in set up/ performance. There are a number of reasons why you're experiencing problems (assuming you are) that are unrelated to the quality of the components. They may simply need cleaning/ relubing/ readjusting.