You said tat you want to upload the components together with the custom module. This sounds like you're uploading the custom module. Can you please elaborate a bit on the approach take. Where would you like to upload these files and will they be used later on by your custom module or application?
So let's see if I got your scenario right - the purpose of your custom module is to upload ascx files to a Sitefinity project. This module is on a different server, not the server, where you have your SitefinityWebApp project (why is that)?Basically, custom modules execute their logic in the context of Sitefinity, so if your module is added to the solution of your SitefinityWebApp project, and you have a reference to it from SitefinityWebApp, then after building the solution, the dll of the custom module will be transfered into the bin of SitefinityWebApp and the code will be executed each time you run SitefinityWebApp. What i'm not sure is how you plan to change the ascx files and make them work in Sitefinity if you aren't building SitefinityWebApp each time you add a new ascx file. Can you elaborate on this?