Well, after tons and tons more of research, I think I may have found a solution. For some reason, PowerDVD was warping the video while playing it like a raised line/bump/hill across the screen, so I ditched that. I tried Stereoscopic player, and I liked that it didn't chop off the sides of the videos (unlike PowerDVD, yet another disadvantage). However, I was still dissatisfied with the quality. So I looked into several other players such as VLC, Media Player Classic - Home Cinema, XMBC, etc., but none of them could readily play 3D without some reworking.
I was ready to give up until I read about Arcsoft Total Media Theatre, which happened to support 3D. I got a copy, and I tried playing a full SBS file, but it wouldn't play. So I tried the 3D Blu-ray ISO, and it played flawlessly and better-looking than any full-SBS .mkv that I've ever had. I also liked how it retained the menus and all aspects of the blu-ray. It was as if I had popped into a 3D blu-ray player connected to a TV. Immediately upon this discovery, I deleted all of my full SBS files and am just keeping the 3D Blu-ray ISOs. It's just simpler that way. Luckily, I don't mind the file sizes of 30-50GB. I also love the amount of features and the fact that the subtitles aren't messed up like they always were in the full-SBS files.
I think I have solved my issue of wanting the best quality possible. I know, I know. Why not play the 3D Blu-ray then? I should probably clarify that I was researching Full-SBS because of the warping the was occuring in PowerDVD while playing the Blu-Ray. I also couldn't get Stereoscopic player to play the Blu-Ray without squishing the resolution. Now that I have a player that plays 3D Blu-Rays perfectly, I feel satisfied.
Thanks for all the help. I actually learned a lot from your post in addition to all the research I did.