I just realized after all these years I never posted a picture of the completed job! I was "supposed" to be moved out of this house by now but thanks to the stalled housing market I'm still here and will get you a "final install "picture. I already posted in this thread all of my "Before" pictures.
To answer your questions:
1. I added a full INCH to my L X W measurements when I ordered the cover. This provided 1/2" overhang on all sides for a wider drip edge and also lots of "wiggle room" in case the chimney was not perfectly square or especially if the flue hole measurement was off. Rockford suggested 1/4" overhang but I was not comfortable with so little margin.
2. I wanted a full brick height to be covered by the skirt so that I had plenty of masonry to attach to. Plus I had to account for the "hump" in the crown, in your case 3". I must have determined my crown's height was 2" and then added a brick height (2"). I posted my final skirt dimensions from the Rockford Chimney order form below and it shows a skirt height of 4". I probably used a long level at the peak of the crown and a ruler at the brick edge to measure the crown's height.
3. I drilled holes in the SS skirt so that the holes would line up with mortar. I then pre-drilled for Tapcons in the mortar. I drilled more holes than probably necessary around the skirt for extra support. I am pretty sure the skirt was already pre-drilled by Rockford but I ignored those holes if they did not line up.
4. I remember spending hours up there measuring, especially to get the location of the flue with respect to the cover edges. This was a super critical measurement.
Bonus suggestion:
Placing the cover on the crown was a PITA and almost cost me my marriage

My wife and I were up there dropping on the cover but it was so heavy and large, it kept flexing into a slightly contorted bowed shape every time we got it where it belongs. It was beyond frustrating. There was no way I could properly line up to drill since it would never rest on the crown's surface properly. We'd get it placed over the flue and resting on the crown, but it would "spring" violently into a slight bowed shape no matter how hard we tried to level it. Solution: I used 3 foot long iron pipe clamps on the narrow dimension of the chimney for the skirt to rest on. Problem solved and marriage saved. Thinking back, Bholler suggested building up and leveling the crown which would have prevented this problem. The cover is so large, on hot Summer days it expands and we hear a loud SNAP inside the room below, which is the cover still flexing up there. Glad I used the extra Tapcons.
The most important advice is to check, double check and re-check your measurements. It may even make sense to make a cheap template out of plywood or OSB which I did not do. That way you can confirm the overhang and flue cutout is correct. It may be overkill but back in 2018 the cover cost me $540.