Are you using a post build event to copy your files up to mojoportal web?
Those paths need to be correct at runtime when they run in the context of mojoPortal. Typcially you don't want to scatter the files for a custom feature all over the place so in your web app you would have a folder for the feature name and all the files for the feature will be below that folder and the post build event will copy them up to the mojoportal web project and they land in the feature name folder there.
ie.
myfeature/
myfeature/UserControls/
and
<%@ Register Src="~/myfeature/UserControls/CommonControls/UcTextBox.ascx" TagPrefix="uc1" TagName="UcTextBox" %>
study the code for existing features like the blog, it has nested usercontrols.
I think the GuestBook tutorial videos would help you.
Best,
Joe