I got the time today to put all the pieces together, hooked the laptop up to the R3, read/saved the existing map (20227). I did ran a comparison with the map I was intending to load (20222) and didn't see any differences except in the mapping for rpm 4800+ and throttle 15%+. I went ahead and loaded the 20222 map. My '05 R3 is currently stock.
The secondaries I remapped manually to much closer, but not quite, to full 100% across the board. Ran the "reset adaptation" and disconnected.
Did a 12-minute tune just to be double sure the changes were recognized and went for a test hop. I could feel a bit more throttle response starting off, but it wasn't huge. I will probably set all the values of secondaries to 100% open soon just to see what that gives me.
Later, I spent some time with the program without the laptop connected to the bike and, with the help of some previous posts, figured out to copy and paste the 4th+ gear ignition timing tables over to the gear 1-3 tables. I also found that you need to right click the O2 sensor box to disable it. Set all the secondaries to full 100% too. Saved that modified map and will give it a try later in the week.