IIS dont function after installing Microsoft sharepoint services

Recently we decided to install microsoft project server for various project management related tasks and timesheet we have to send to client. We decided to install it on windows 2003 server with sql server installed on it. Unlike other microsoft products, installation process was not something like you sit back clicking next - next and next. Although project server 2003 installation guide has detailed step by step information, it was not a smooth and easy installation.

Microsoft Project server requires installation of Microsoft Windows Sharepoint service for document management. Integration is really good. But after installing share point service, IIS stopped functioning. We did following to make it work :
- Remove default website from sharepoint service

Now other sites which were hosted on IIS stopped working. Bydefault all websites were in website pool created by sharepoint.
- So we changed all websites pool to default website.

All gone well and after wasting whole day project server was working fine. But suddenly found a new problem. Visual studio is not allowing to debug any prjoect. There was a problem of trust level, which got removed after putting below mentioned line in web.config

<trust level="Full" originurl="">

Atlast, there was no other problem and all is working smoothly. Though, i would have loved to have a totally web based project management server rather then web+desktop integrated product.