Hello Colin,
Putting the DNA filter question to the side, as I have no experience with that accessory, I do think that you need to listen to your engine more, when it is causing the mirrors to vibrate, because it is telling you that you are lugging the engine. Focusing on the speedometer and going by the
very conservative maximum speeds per gear, as given in the manual, is really not exercising that engine at all. You are doing more harm than good.
I change gears according to the sound and feel of the engine. More sound than feel really because my Meteor has very little vibration anywhere, that I have found up to 60 mph, so far. I also pull away and accelerate smartly through the gears, rather than with a low throttle/slower gear changes style of riding. One thing I hate about some cagers is the city block that it takes them to get up to the damn speed limit from a stop!
However, reading your post early today gave me the thought to actually watch at what speeds I was changing at, to compare with your figures. My first ride of the season too! Wooooo-Hoooooooo!!
Here's what I noted over 2 hours of riding today. Second gear is engaged at 25 mph. Third gear at 40 mph. Fourth gear at 50 mph and fifth gear at 55mph, as long as I am not going up a hill. The engine is not wrung out to the max (not full throttle) in each of these gears either, as there is still more revs to go before the engine would hit the rev limiter. I just turned over 600 miles today and that engine loves to run! It is very perky when you feed it well!
You need to allow your engine to rev more for its better health.