I understand the situation, many other websites have similar issues. But there are options, even if you have many backlinks pointing to DC pages:
1) Like you made 301s from other Codestore domains to the www.codestore.net domain, do so for the pattern www.codestore.net/store.nsf*. Assuming ofc. you want www.codestore.net to be the homepage URL (recommended), otherwise the other way around.
2) Make sure all internal links to your homepage goes to the correct URL, as Yahoo Site Explorer suggest you have many internal links pointing to both www.codestore.net and www.codestore.net/store.nsf/. It could be you already rectified this (I didn't check) and Yahoo Site Explorer just haven't figured it out yet.
301s will transfer link value (as indicated by the visible Google Toolbar PageRank), but - propably - not 100%. Another drawback is the added round trip, making 301 pages slower. Still, 301s are the best option for situations like this.
Btw., an annoying thing about the trailing "/" in Domino is that these 2 URLs:
- are technically different URLs, but Domino does not seem to care about the trailing slash at all. I have not managed to find suitable substitution/redirection documents to fix this issue.