Hello, fellow Avail 3 owner! (Mine's a 2009.) That's a really pretty color.

Generally, the advice is that if you're between bike sizes, to size down. (I'm in the same boat--I'm between a small and a medium in Giant's sizing, and while I'm riding a medium, I should be on a small.) I (or, I should say, the BF) took the toe cages off mine when I got it; wheel reflectors came off last summer after one broke and I helped the other one along.

You might be able to get the 28s in there, but don't count on it. 700x25 is generally the widest tire that road brakes will take. Certain 28s might work (because there's no closely-followed standard).