I'm not a GI fellow but i can share with you what i came up with from asking around (since i graduated from a small community hospital)
1- i think if you swap to a program that has the fellowship that will be the best thing you can do. most of the GI programs offer 1-3 spots per year, and assuming that that hospital already have a residency program, there is at least one spot going to their resident (so this can be you)
2- Research, Publications, Connections sounds like a big player in your application if you are comming from an "unheard of" hospital. dont waste your 3 years of residency chasing social workers to help discharge your patients so that you can have a low census list.
mmmm, i dont know what else i can add to that