Go for it. It's a lot of fun. I've made five so far (all guitars). If you want to get adventurous, get an unfinished body and do the painting yourself. It takes time, and makes a lot of mess, but it makes it more fun and more [b]your [/b]guitar. I did that on two of them, and I like them the most.
There are downsides, though. Resale value is low, so you will either have to part out the guitar on Ebay or watch it sell for 10% of what you paid for it*. It will also most likely not play well unless you take it in for a good setup, as simply bolting a neck on to a body does not a magical guitar make, so factor the cost of this into your budget. You could do the setup yourself, but you may want to get it done by a pro so it really is good. You can also hit compatibility problems too, even if you, say, only get Fender parts. The hardest thing I found was to look beyond the sentimental and try and look at the project objectively. No, it is not as good as a Custom Shop model. You will forgive your project for any minor flaws, but that doesn't mean it's the best thing ever made!
*Although there is no way I would ever sell any of mine. No way. They are like children to me.