Between the end of Season 1 and the beginning of Season 2, Jake goes undercover for 6 months, but in 3.17 Holt and Jake talk about how he was undercover for 63 days, which is only about 2 months.
Captain Holt wears his Commendation breast bar above his World Trade Center Breast Bar. When the WTC bar is worn, it is worn above all other medals but below the American Flag bar.