I am a bit rusty as well with putting back stock stuff on an ox'd system. I guess the first thing I would do since it sounds as if you may not have written down everything you removed is to do a side by side comparison and make a list.
As to getting them back, I know for sure that it would be safest to adb push the stuff to system, and get the permissions correct. You might be able to install the apks, but not sure on that. You can also try just copying them back in place with what ever root file manager you used to remove them, and set the correct permissions. But I will caveat that with again not having done this in a while, you do need to be careful replacing files in the system, while it is running. I am sure some of the less inocuous apps would be ok, but you need to be careful if you hammered away at more of the integrated system apps. There have been a few folks in the D3 forum who have done this, if you do not get additional info here, perhaps IM one of them to see if they can help. I just tend to be very careful right now, as soft bricks are pretty easy to do.
Actually if it were me, I might consider doing nothing, as any OTA does not appear to be immenant, and by the time the first OTA does roll out, there may be other options. If your phone is running correctly, it might be safer. At this point we do not even know for sure what will happen with any OTA's.