The term "1800 CVO" in the TTS cal file listing document generally means a stock 110" engine with the stock 2-1-2 exhaust, cams, and breather - because thats what CVOs come with now.
The EUK009-03 cal file is not the right one for you to use for your basically-stock CVO Ultra. It is for a modded engine with much higher duration cams, head work, big injectors, etc. Your stock 110" engine would be swimming in fuel with that cal file!
For a 2011-2012 (or 2013) stock CVO Touring bike, it says to use the ETA044-03 cal file to start. That's the one you should use - because you have a stock 110" engine with the stock cams for CVOs, which are SE 255 cams. The mufflers are not nearly as important to the calibration as are the cams.
Also, if you are to remove the cat from the head pipe, I would do it before I bothered with VTune - so you don't have to do more VTune runs after the exhaust restriction is gone. A freer-flowing catless exhaust will change the breathing characteristics of the engine significantly, requiring more VTune runs.
The following text (in purple) is from the TTS cal file listing document:
How To Select Calibrations
Note:
This calibration listing is intended to be used in conjunction with the TTS tuning guide, “Using MasterTune and DataMaster to Tune Harley-Davidson Motorcycles”. Refer to the tuning guide for details on setting up calibrations to work with your specific vehicle.
As a general rule, use the following selection priority if your exact combination is not found. This works for most builds.
1. Match the vehicle year and model to get the correct calibration level (i.e.176, 205)
2. Match the camshaft selection (if not stock) as close a possible
3. Match the head configuration (if not stock)
4. Match the exhaust configuration
If the engine displacement or injector flow are different, you will adjust this in the ECM constants.
Note that the camshaft selection affects the vehicle’s breathing and part throttle drivability more than any other factor, thus is the most important factor to consider for your starting calibration.
If you are using VTune, several VTune iterations will be required to adjust any calibration to match your specific vehicle. Refer to the tuning guide for complete details on setting up a calibration for VTune.
As the document says - the cam selector settings for the cams you have in the bike are the most important thing to get correct first in the calibration. So, the first thing to do once you have flashed the starting calibration into the bike is to do a CamTune run to determine the cam selector intake valve opening (IVO) setting for the calibration. If this setting - along with the intake valve closing (IVC) setting - are not correct for the cams you have in the bike, then nothing else really matters, and you will be wasting your time trying to use DataMaster and VTune later. They can't compensate for incorrect IVO/IVC settings in the cam selector part of the calibration. You can use the "cam estimator" function in MasterTune to,determine the correct IVC setting (and IVO setting too, if you really don't want to do a proper CamTune run to determine it.)
The cam selector settings in the ETA044-03 cal file are correct for the stock CVO SE 255 cams - but if it were my bike I would do a CamTune run anyway - if only to verify that these settings are what your particular engine really needs. It only takes a few minutes to do a CamTune run, and then you know for sure what cam selector values you need to use.
Good luck!