Lil,
I am a little confused. The apps that you deleted should be in /system/app. The only download folder I see is in /data/app. The data partition (subdirectory) is where the applications that you download from the market should install. The applications in /system/app would be the ones that came installed on the phone, in this location. If the programs that you reinstalled are in /data/app, then they are not in the original location.
As to your adb "install", I think that it would attempt to install in data. Just a guess here. If I were trying this with adb, I would try and push to system and change permissions from adb, if that is possible. This should be similar to using Root Explorer to move it over, and change permissions. It is just that using Root Explorer on a program integrated into the running OS can be risky or not possible in some cases.
BUT, that file/application has an ominous soundiing name, I would perhaps check in the D3 hack subforum to see if messing with this file would be problematic. If you are trying to uninstall this application from the application menus, it will not uninstall becasue it is part of the Bloat. But I use bloat loosly, as I do not know if this file is more integrated into the OS (soft brick?).
It looks like a custom recovery may be getting pretty close. If this does happen, perhaps some generous soul will create a "stock" backup of the phone (less personal accounts etc.) and make this available for folks who are trying to recreate the stock system. I only mention this, if you are doing anything that you feel uncomfortable about. Having a custom recovery is one step closer to the dev's being able to snag any OTA, root it, and let it out for an install, bypassing a lot of this concern about phones not getting any OTA.
As I mentioned earlier, it might be best to sit tight for a few days, especially if your phone is running correctly. We will have plenty of notice before any OTA is released.
Craig