Hmm... I am excited to see an Alfred Chicken run and have worked a bit on the NES version as well, but it looks like this run could be optimized quite a bit more. I also question whether an optimized run would be accepted, although I personally think it should be.
Here's a WIP of the first level that completes it over a second faster, if my math is right:
http://dehacked.2y.net/microstorage.php/info/1367716681/Alfred_C_alden.fm2
And here's an almost real time demo I made just now of a shortcut in the water section of the second level that saves over 30 seconds:
http://dehacked.2y.net/microstorage.php/info/1478147870/Alfred_Chicken_Shortcut_alden.fm2
I honestly didn't watch the movie past that point so there could be other big timesavers, but I found that shortcut in a FAQ on the Internet, so with a Google you can be as much of an expert and I am (not really much of an expert at all).
I hope you'll keep working on this and post some WIPs the forums!
Edit: Oh, haha, I just realized Ferret posted a wip too... his first level is clearly even faster than mine (though he missed the water shortcut too :P)