If it works on windows why does it need the server at all? If it is just making requests to Apple can't you do the signing on the phone? (Other than the bootstrap procedure)
AltStore is based on the signing code I developed and also used in my Cydia Impactor (which lets you install apps over USB); I actually did develop another tool called Cydia Extender, which would run on your phone, but I dropped the effort when I couldn't get stuff to install on the phone (the technique I came up with relied on an entitlement that was only able to be installed by users with developer accounts; I even somehow failed to notice this until after I released it, which was awkward: I still can't believe I messed up my testing that badly). (Actually... maybe I have a way to pull this off now? It is a long shot, and somewhat risky ;P.)