If you have the funds for a full custom build then go for it. In the long run you will be happier and will be upgrading or swapping parts less.

To put things into perspective. I put together a full Soma Rush build over three years ago and spent around $1,300 but I was extremely happy and never had to touch anything after I first built it. However, I also recently purchased a complete Soma Rush build on Craigslist for $290 so I can swap frames... Granted, the used CG build didn't have as nice of parts as the build I put together but it did come with Omniums, Gatorskins, Fizik Bars and Velocity Deep V wheels.

If you can find a good deal on CG that's similar to what you have in mind you can save lots of $$$