Finished!
http://www.lockntoad.com/homyguyz/amhaynes-ewj2rough.smv
I'm going to go back and hexedit it to redo Blind Sally and Flyin' King before I submit it as I mentioned, and See Jim Run has a moment where I pause before a jump by accident that I'll go back and fix, but other than that this is the complete run. Oh, and the movie end is in a weird spot because I skipped past the last cow image out of habit, I'll fix that too. Comes out to be 41:08 with 148105 frames and 9132 rerecords.
A few things of note: In Udderly Abducted there's a few spots where I jump/whip for seemingly no reason, it's to stop the UFOs from lifting the cow so I can pick it back up. And in the fight with Flamin' Yawn at the end of Level Ate it might look like I missed, but I actually went through it a couple of times to be sure of the number of shots needed to kill him, so I'm still connecting. I tried to avoid taking damage where I could, but I'm a little inconsistent on where I shoot for best time and where I try to make it look better by avoiding it. Level Ate especially is a little weird about this with the eggs on the frier.
Let me know what you think, the full submission should be ready pretty soon.