Is there a site that can help you with compatibility among all parts?
There are sites that will let you pick all of the compatible components for a bicycle.
The following are sites built by people who want to make money selling you a custom bike (these are examples of bike builder apps, not recommendations).
Fanatic.com has a bike builder feature on their website for mountain bikes for a specific set of brands.
Wrenchscience.com also has a bike builder on their website for a variety of bike types and brands.
You can build a bike on these sites and then use the list of parts to purchase from whomever you like.
For an example of a bike builder that does not appear to be tied to a store.
Bike Config is a 3D app that custom builds a bicycle. It appears to be all mountain bikes with a limited list of parts but they hope to grow.
Searching "build a bicycle online" will deliver these and other options.