Well I have two comments that may or may not help.
1. I'm not sure how you determine when to add water, but if you're not adding it at least daily, I would start there. I know when I had the 29 Cube and now my 32 Rimless I evaporate about 10G every 2ish weeks. A half gallon swing per day in a small tank is a LOT in regards to parameters.
2. Based on the age of your tank and your current parameters I would look into possibly increasing your WC frequency to weekly instead of bi-weekly. At 20 Nitrates and .1Poshphate those aren't dangerous levels for BTAs, and I've seen tanks with higher, but I would assume things are trending upwards if you were to chart it over the last 3 months or so.
In my small 32 if I change my water every week my nem stays happy and my numbers stay consistent. If I miss a week and it gets to two weeks, my nems starts looking mad and it's a pretty tell tale sign that he's not happy with the current conditions. I would assume you're experiencing the same thing here.
Secondly, you're going to need to figure out a way to get him to eat. Not sure what you feed, but some LRS/Mysis/Krill...etc, something you can put in a baster and squirt at the mouth once or twice a week would do him a world of good.
Thirdly I would back off on your acclimation and kind of do a reset. If you read through the installation guide for this LED (Which you can find
http://stevesleds.info/downloads/biocube-29-coralife-fully-loaded-install-guide-572017.pdf ) you most probably went too fast.
Which kit LED did you upgrade to? Was it the Steve's kit?