You should be able to find a 90 degree transition that is 3.25 inches high. You could also connect it with a piece of flexible duct. Below is a kit made specifically for this purpose. Here is a link that might be useful: Toe kick duct kit

Thanks all! Babka, signature hardware has a wall register that is 2.25x10 with overall dimension of 3.25x11.5 that looks like it will work, I'll just have to call tomorrow to see if it will fit in my baseboard hole because it is meant to be centered on a hole in the wall rather than placed in a toekick. I may have to do a modification on the toekick, I was trying to avoid that. I would be thrilled if they just had the plate without the damper attached to it, that would simplify the issue. This post was edited by detroit_burb on Sun, Aug 3, 14 at 13:42

"he cut the toe kick so my arm is between the bottom of the cabinet and the top of the vent." So you can remove the old toe kick and replace it with a new one? Then I'd (1) remove the vent cover, if any; (2) remove the toe kick; (3) carefully measure the width, height, and location of the duct; (4) cut the new toe kick for the duct (example); (5) slide the new toe kick over the duct; (6) attach the toe kick to the cabinet; (7) attach the vent cover to the toe kick. "contractor installed a copper pipe...and it's sticking out pretty far" The pipe IS going to be copper. The finish on the fixtures is irrelevant. It's better that the pipe be too long than too short. If you ever have to cut off a valve to replace it and the remaining pipe is too short, you'll be in trouble. (Here's a video that shows how to replace a valve.)

@Seabornman I will have AC as I'm having a heat pump installed, but I think I'd probably have the vent closed when the AC was on, because I hate having it on my feet. Would you still recommend using an insulated one knowing that? Also, the rest of the ductwork isn't insulated. Is it something I should look at doing before summer hits? @mike_home those toe ductor kits are the first thing I found when starting to research this, but as you noted, it did look like something to use before the cabinet is installed. It was watching the install videos that led me to my original question on this post - do I even need to add a boot on either side of the ceiling/floor, or could I just run one piece of flexible ductwork that I could flatten a bit at the end to fit. Like how the toe ductor vent is more oval shaped at the end. @Mark Bitman why is flexible ducting a problem?