Stupid Maintenance question

Step one should be to buy Zinn and the Art of Triathlon Bikes. 

Yeah, you'll have to pull the cables.  As for getting the bar end shifters off, you'll be removing the lever, then using a hex key to loosen up the star nut so you can pull them out.

As far as the price goes, I recently took by road bike to the LBS and had them change the bar and also install aerobars. I also bought brand new tape, new end caps, and an aero-bottle. They charged me $70 for the entire installation and new tape and bottle.

$100 sounds steep to me, but your setup may be more complicated than mine.

I've never run cables internally, but I do know that Zinn gave some good tips on how to do it.  Here's what I would do:  Tape some string to the end of your cable that's on there already.  Pull it out through the frame so that you basically now have internally routed string.  Untape the cable from the string.  Tape the string coming out of the ends to the frame so it doesn't fall out when you change the bars.  Pull your cable through the bars and shifters, change the bars and shifters, run the cable through the bars and shifters.  Retape the cable to the string.  Pull through carefully.

Nothing on a bike is really that hard to do.  Some of it may be more time consuming than paying the bike shop to do it, but you definitely can do it all yourself.  Just get that Zinn book and have at it.  You'll use it for far more than just this bit of maintenance. 

Any big chain book store would probably have it in stock.  If not, they'd order it for you or you could just go home and order it online.  You ought to try to do it yourself, then if you eff it up, just take it to the LBS.  It would be a good learning experience at the very least.

Oh, and even if you don't try it, I still suggest the Zinn book.