I would recommend that you work with Tech Support on this issue. You may or may not need to get your SAS administrator involved in making sure that the servers and repositories are all defined where they need to be defined. I'm not sure whether a custom repository's stored processes are visible to servers under the Foundation repository application server context. You might find the answer in the Platform Administration documentation.
Overall, Tech Support will be your best bet for help with this question.
I believe that SP:s only can exist in Foundation, well I had never come across any other implementation. As a general
rule of thumb: unless specified, all EBIS objects must reside in Foundation (9.1.3).
This is really a question for Tech Support. In the glossary
( http://support.sas.com/rnd/itech/doc9/glossary.html#C ), it says that "A custom repository is used to specify resources that are unique to a particular data collection." I believe -which- resources are available depend on your configuration, security and server setup.
There are SAS solutions, such as ITRM, that run in a custom repository and have stored processes. I am not sure where the stored processes "live" -- in the Foundation repository, or in the custom repository.
I really think you should contact Tech Support to open a ticket about this question. When you are building the architecture for an application or solution, it is better to get the final word on what's possible or not from Tech Support -- because if they do not know the answer to your question, they have the resources to get the definitive answer to your question.