Using my Roster Editor I was able to assign most of the 2nd rounders and missing players to their respective teams, or to free agency if they didn't fit the team's roster.
Note that most missing players added have the same generic ratings. Most have CFs and portraits, some don't, some have CFs assigned to Baumgartner's for whatever reason.

I used this thread as a guide as to who to look for.
I hope this proves to be a nice base for roster makers to give us some nice full rosters without needing to do too much CAPing. I also hope to be able to find the CF parameter in the player entries soon, so that we can fix the missing CFs.
Here's the list I created from that thread. Players I found in the roster have an ID and a status to them. "A" is for "assigned to team". Players without an ID and status are players I couldn't find in this run through the roster. Unguaranteed players are added to their teams if they fit, otherwise they're released to free agency. Some guaranteed players didn't fit their respective team's roster either, but I've released them to free agency, so you should be able to fix the rosters and get them in.
https://docs.google.com/spreadsheet/ccc?key=0Ai16USDxg1E8dC1uUmNYeWZhLWdxYmxUTE9qTTBqbUE
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Base Roster (Most Missing Players Added)