Okay, so I finally completed this task by doing the following:
I contacted the Boyce Thompson Institute who ran the Sol Genomics website to see if they had any conversion sheets from their Sol genomics IDs to something more common. They sent me a very good conversion sheet of Sol gene IDs to UniProt IDs.
If someone knows how to share files on biostar I'll attach the conversion sheet to my answer. It's 1.7 MB, so not too big. I can't find the same file in the Sol genomics ftp directory, but I haven't looked that hard either. so if someone knows how to share files like this or if the file is on the sol genomics ftp directory, any help would be appreciated.
So I got my sol gene IDs, got the sol to Uniprot IDs sheet, and used Galaxy to convert the sequences with the info on the conversion sheet.
Most gene enrichment analysis programs take the UniProt IDs, so this conversion did what I wanted it to do.
Also this web based program can do Gene Enrichment analysis using the Sol gene IDs: http://bioinfo.bti.cornell.edu/tool/MetGenMAP
Another good program that can use the Sol gene IDs for gene enrichment analysis: http://mapman.gabipd.org/web/guest/home
So that's how I solved my issue. Thanks for the help guys.