I've built up several bikes,and more often than not the builds cost more than the stock bikes. I tend to use better components than the stock bike and STI shifters which add to the cost. This is the case even though I pick up most of the parts online, get a discount at my LBS, and buy when parts are on sale. However, the bike is really dialed in to my needs, and it is worth the extra cost.

This is very important, especially if you are using STI shifters and want to have mountain gearing on your bike (44/32/22 cranks). However, I believe that you have to have more than a "bit" of skill to do a really good job, not to mention a pretty good complement of tools. If your LHT frame is new, you will probably have to have your bottom bracket threads "chased" and the BB "faced" The tools are expensive, and the LBS usually charges $25-$30 for the service. Installing headsets also require some skill to do it right, and specialized tools make it a lot easier.

Having said all this, building up you own bike is a rewarding experience. Also as mentioned the knowledge gained is good experience when something needs fixing. The tools you buy are a good investment.

A good compromise might be to work with your LBS on component selection and have them do the build, with you assisting. The extra cost could be "written off" as education. You would also get a good idea of the tools necessary to do future maintenance. You can also try different sized stems at the LBS as you start to dial in your fit instead of guessing when you order it.

Good luck to you regardless of how you decide to do the build.