To alleviate your confusion, I'm not talking about the /system/app or data/app in this case. The apks are DEFINITELY in the /system/app folder.
I'm referring to viewing the apps in home > settings > applications > manage applications...
Before removing the bloatware, only the apps which I downloaded from the market were in the first tab of that screen which is the "downloaded" tab. Those apps were in the next tab, "all" which includes preinstalled bloatware apps and downloaded apps.
Now, after reinstalling those apps (which are in the /system/app folder), they show up in the "downloaded" tab. This means the phone is still seeing them differently than it was originally. I think this is because of the permissions still being different than they were when I started. I won't have time to mess with that til tmrw morning, unfortunately.
As my phone is working just fine, I'm fine with hanging out til someone releases a stock backup or an SBF is released. I just like knowing how to fix stuff if I have to!
As for the app with the odex file associated, I believe it still needs to be installed in /system/app where it came from. You think it should go in the /data/app folder?