Locally the Republican Party has complete control over the Independence Party. You have to look long and hard for the last Democrat endorsed by them. In 2007 all 19 of the Republican candidates for County Leg got the Independence endorsement and it went so far that the Chairwoman of the Party was also on Jim Walsh's payroll. So going into this Congressional race, you would think that the Republicans would give their candidate of choice the Independence nod, but not so fast.
Rewind to the Special Election for the 48th Senate District a few months ago. The Oswego Independence Party magically appeared and endorsed Will Barclay, the Jefferson County Independence Party, the only previously constitute IP in the district, responded by endorsing Darrell Aubertine. Under past rules, the Oswego County IP would determine the endorsement because the most votes for Governor cast on the IP line were in the Oswego County portion of the district. A series of court battles ensued, and eventually Barclay was put on the ballot by the courts the night before the election. (Side note: the NYS Dems screwed up the lawsuit by having Aubertine sue rather than an IP member, and since Aubertine wasn't an IP member he had no standing to contest) Anyways in response to all this, the State organization of the IP decided to change rules.
So while just a few months ago the Republicans in Onondaga County could name their candidate for Congress to the IP line, now all endorsements that cross county lines are made by the State Committee. And unless there is a strong force, like Joe Bruno, pushing a candidate, the IP will likely side with the candidate who looks stronger. With Dan massively outraising his opponents who collectively have 0 dollars, and the next filing period not until after petitions have gone out, the IP will be hard pressed not to endorse him. And it is all because of the Darrell Aubertine and the Jefferson County IP. It should also be noted, that Jim Walsh took 7,700 votes on the IP line in 2006 and he won by just 3,400 votes.