Unless you’re editing the comments, IMO you didn’t get your money’s worth from the judge. I’d expect a lot more description than you got from a National level judge, and I really hate vague, unhelpful terms like “funk.” If this guy was proctoring an exam beer, I’d be swearing at him through the entire exam set as I graded it. He might be Nationally ranked, but he wasn’t up to scratch when he scored your beer.
Given that your beer’s a strong Rye IPA, possibly made with old hops, and possibly fermented too warm, there’s at least six things that could account for the “funk” and he didn’t mention any of them in aroma, flavor or overall impression.
Other folks have hit some of the points, I’ll try to fill in a few more.
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Rye + Acetaldehyde + American hops - Spicy rye plus green apple plus citrusy piney hops could throw some unusual flavors and aromas that even a Grand Master might not be able to sort out.
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Old Hops - If you got a good deal on Willamette, they might have been old or improperly stored. If you got notes like Roquefort cheese in the aroma or flavor, that’s a telltale sign of old hops. It’s subtle, but definitely “funky.” If you have any of the suspect hops still around, smell them - really huff them to get the aroma deep into your nasal passages. If you pick up cheesy and/or grassy notes, and/or if the hops are brownish and fall apart easily, you’ve got old hops.
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Phenols + higher alcohols - The classic sign of beer fermented at too high a temperature, or stressed due to poor yeast management, is phenols and solventy notes (along with esters). At low levels, masked by high hopping levels, they might also be perceived as “funk.” If you’re brewing a big beer like the one you describe without making a yeast starter and fermenting at possibly warm temperatures or in an environment where there could be temperature swings, you’re just asking for trouble.
Even so, you got a decent score for aroma, so my guess is that the judge was just describing the hop character. Sometimes American hops can indeed smell “catty” or sometimes like fresh marijuana (which often gets described euphemistically as “dank”).
Other folks have mentioned the acetaldehyde problem. I agree with the people who say it’s a fermentation problem. If it was an infection, the green apple notes would come with prominent sour or unpleasant sulfury aromas. My guess is that your sanitation’s just fine. Any sanitizer works just fine if you’re using it right.
Probably lost a point here for low carbonation levels and haze. An IPA should have a thick, lingering head.
Very hazy could mean a number of things. Slight hop haze is OK in this style, but turbid isn’t.
Does haze clear as the beer warms? If so, you’ve definitely got chill haze - which would also explain the astringency problem. Be careful to not let the temperature of your grains go above ~168-170 *F, that’s the big astringency producer. Other tips: recirculate your runnings until they’re clear before running them into your boil kettle. Don’t grind your grain too fine (bits of powdered husk can get into the boil kettle). Don’t collect runoff below 0.08 S.G. Don’t let your runoff pH rise above 5.8.
If the haze doesn’t clear once the beer gets closer to room temperature, it’s probably protein and/or starch haze. Not surprising for a rye beer which is high in both. If you think the haze is a problem and you have the technology to do so, consider a protein/beta-glucan rest @ ~120 *F for 15-20 minutes, before stepping up the temperature to starch conversion temp.
Low CO2 might not seem like a big deal, but flat beer doesn’t outgas as much, so it decreases aroma. Lack of CO2 also changes flavor perception and mouthfeel, making the beer seem sweeter and fuller-bodied. Since you’re kegging, it’s easy enough to bump up the CO2 before you bottle for competition.
Here’s where you got killed on the score. 12 out of 20 means that the judge got a serious letdown between smelling the beer and tasting it, putting flavor on the low side of an average score. You probably had solid malt character (nothing wrong with your malt bill) since there were no comments criticizing it, but if it’s an American IPA the tropical notes are out of place (unless they came from hops). Fruity notes are from esters, which point to problems with fermentation temperature; Safale-05 should give a relatively neutral (i.e., not a whole lot of) yeast character at proper fermentation temps.
No mention of hop flavor except in the finish could have been the judge phoning it in, or it could mean that you’re not getting as much flavor and aroma out of your late hops as you might (although your hopping schedule looks very generous). Again, this could be old hops, or it could be beer that’s past its peak or otherwise oxidized. If the beer was at the peak of freshness, consider dry hopping to get more hop complexity. If you want to get fancy, you can also do first-wort hopping in addition to everything else. Basically, use any trick in the book to get that hop character.
The judge mentions CO2 being on the low side, so that’s definitely a problem. The slight astringency could be due to hops and/or minerals such as sulfates which can enhance perception of hop dryness. As long as your mash technique is good I wouldn’t beat yourself up about it.
No suggestions for feedback here from the judge, unless you’ve edited the comments. That’s very bad form on the judge’s part.
My guess here is that the judge was impressed by the malt character, although he didn’t say much about it in the flavor and aroma sections where it belongs. If malt character was dominant in what’s basically a strong Rye IPA, that might mean that you’re not getting as much hop character as you want. Or, it could just be referring to the rather chewy, slightly caramel malt character underlying high hopping levels.
The judge didn’t add his score right. It happens. Give yourself the benefit of the doubt and call it a 32.
My ignorant guess is that you could bring up bittering hops (or, rather, bittering IBU - less green stuff, more alphas to reduce hop astringency) by 0.5 to 1 oz. and perhaps add 0.5 to 1 oz. of dry hops in secondary.
Also, if you’re consistently getting extract yields below 60% range, you’re doing something wrong with your mashing technique.
This could be something as simple as not mashing for long enough (go for 30-60 minutes), a mash tun that loses too much heat during mashing (unlikely, though with your setup), not sparging long enough (go for a long, slow runoff - 30+ minutes) or poor grain crush (are you using a Corona mill?)
Another possibility is that your thermometer is calibrated incorrectly, so you’re hitting temperatures way above or below starch conversion temps. I speak from sad experience! 
If so, that would also account for any starch haze you’re getting (i.e., in beers made without grains like wheat or rye).
Not really. Cara- malts are more for body, crystal gives more sweetness and specialty malt flavor and aroma.