My rogue trader has an incompetant crew on his ship (their competency was sacrificed for five additional ship points during the character generation session).

Are there any provisions in the rules anywhere for taking my present crew and making them better? (They've got cool traditions, they're loyal and I'm not replaceing them.)

There's an example for you: my loyal scribe misspelled "incompetent " and put a capitol H in the middle of the title for no good reason. Yet I'm not willing to shoot him and replace him with a servitor. (He makes excellent egg nog, much better than I'd be able to get from a servitor).

You might be able to train them...firing drills (just watch Master and Commander), manouver drills, combat drills....just training...
To raise their quality since training costs money would be good roleplaying and an Acquistion Test

I treat it as a set of Acquisitions. Going from Incompetent to Competent is 5 SP, and I choose break this down into five Rare Acquisitions (each as per Essential Component, +1 SP). I then go with a variation on the time requirements based upon how much the ship is doing - each of these Acquisitions can take from three weeks (constant training drills and minimal other activities) to six weeks (ship is working towards objectives, performing extended repairs, or traveling through the Warp). Going from Incompetent to Competent using this takes a minimum of 15 weeks assuming the vessel is focused exclusively on the training and all Acquisitions are poured into improving the Crew Quality. Oddly enough, that's just a bit longer than the length of many bootcamps.

Sounds like I am running things similar to others. It isn't a single aquisition, it is something you actively work towards.

Time and money needs to be spent on training (aquisition check and command checks), and the costs and difficulty go up for krak and veteran status. The Captain needs to go out of his way to provide real world opportunities to practice (i.e. think to get them out there and do stuff, even it it isn't strictly necessary). Finally, they just need experience. I would require 6 or so sessions of this type of behavior (for a weekly game) and then allow their skill to increase.

Usually, i just use travelling time for some training role-playing. Gun-Drills "run out the macro-cannons, you dogs!" and so on. after some training time and two or three space battles, I`d go for a aquisition test.