Performance wise, it's a tricky one to answer, as it's very depending upon how your custom solution is developed, what hardware platform you're planning on deploying the solution to, etc. I think most people would agree that, in general, MOSS will be slower than an ASP.NET application written in house, primarily because it's unlikely to be as complex and expansive as MOSS.
That said, it's very easy to deploy MOSS across a network load balanced farm (obviously increasing the licensing costs significantly), and share the load that way, thus getting a pretty significant performance boost over a more traditional ASP.NET app deployed to a standalone server.
As others have said re: development, it's incredibly dependant on what you're actually wanting out of the end solution. As Dr said, it would be a major development effort to reimplement some of the core MOSS features, such as it's Office integration, it's document management, version control and fine grain permissions.
If you feel that you're going to have customise a large chunk of MOSS, then the development effort can be quite involved, especially if you don't have anyone in house familiar with the process. It's a big product, and finding your way around it's innards and API is no small task when first starting out.
I should mention that we've had a lot of clients who have gone into MOSS evaluations thinking that there will be a significant amount of work customising, etc, but not realising that actually, 90% of what they want to achieve can be so with minimum development efforts, it's usually more a lack of understand of all the options available to them within MOSS.