[querty1000]

1) Can Kodi not play AVC-1 encoded files? Quite a few of my blu rays (from my collection) are ripped in this format. When I try to play them, they just display a light purple screen. This was not the case with XBMC on my home PC.

about wich KODI we are talking about? Latest nightlys or old outdated google store stuff?

2) I've tried and tried but I cannot get my projector to recognize any 3D files, played either from video add-ons, from my HD, or from Youtube. The files I'm trying to play from my HD are downloads (typically around 1.5 GB) of mostly side-by-side content and they're named using the proper file naming (name.3D.SBS.mkv). It seems the projector doesn't recognize them as being in 3D. I can play blu rays directly from my blu ray player and the projector recognizes them immediately and goes into 3D mode. The projector is the JVC RS400. Anyone know what's going on?

You should in meantime not proper mark the 3D files as 3D since the shield have some issues about that. If KODI thinks the files are plain 2D files, you can decode the both halfs of the picture by setting the TV or projector by hand.

I'm using the original kodi that I downloaded to the box from the android store. I'm assuming that's what you mean that it's outdated. Excuse my ignorance, but how can I install a better/updated version? A guide would be much appreciated. Also, can any of the updated versions play this type of file?

Thanks!

If you wan't KODI 16, wich is almost ready and in RC2 stage, you should follow this thread:
252852 (thread)
but the sound is implemented a non-official way.

If you wan't an official KODI with passthrough sound you have to use the Krypton Early Acces (or newer if avail) from:
http://kodi.tv/download/

The Krypton nightly will in the next night implement proper Android sound like the KODI 16 build.