Yes and yes. It would read the map it had no problem but wouldn't download a new one or so recovery mode without the fuses back in. Goin to try a different map tonight that looks better suited for me and I will leave the fuses in for the whole process and see if it works without issue again.
I just checked out the Roadster tunes on the TuneECU site. This is for off road mufflers (TOR). The K&N filter doesn't matter.
For VINs up to 574812 they say to use 20355
For VINs after 574813 they say to use 20688
The only difference I can see between the 2 is that 20688 has the secondaries open 100% in all gears up to 4600 rpm above which the secondaries are closed down in 4th and 5th. As I noted, you will be at 100 mph by this point. The 20355 tune has the secondaries closed much more in 1st-3rd.
The fuel and ignition tables are exactly the same between the two tunes.
TuneECU allows you to compare these two tunes but that doesn't necessarily mean that 20688 will load into an older Roadster.
However, if this is the case, just bring up 20355, open the secondaries 100% in all gears and rpm, and use it! If 20688 will load, first open the secondaries 100% in the cells where it's below 100% and use that!
As Barbagris noted, the O2 sensor signal is used only under low load which is throttle position less than 35%. It tends to lean it out under these conditions but under hard acceleration, it uses the main fuel table and the O2 sensor isn't used.
In my 2005 R3 with TORs and cat bypass, leaving the O2 sensor hooked in made it run smoother at low load but caused backfiring in the pipes. This can be annoying but it doesn't harm the bike.
Unless you modify the exhaust and/or intake further, just use one of the stock Roadster tunes with the secondaries open at 100% and leave the O2 box checked.