Put it on your layout, run it and have fun, no one knows but you. The casual observer will say I saw the engine in real life. Enjoy it, looks great.
Dennis reminded me of an automobile manufacturer's (will remain nameless) old adage regarding such 'nits', told to me when I started work there nearly 60 years ago...
"If you can't see it when the car goes by you at 60 mph and 100 yards away, it's good to go!" Of course, all that changed in the worldwide game of competitiveness...bar-raising expectations among manufacturers and consumers...etc., etc., blah, blah.
So, when you invited our opinions showing us only the close-up views of the minutiae...your self-critical irks..., you were setting yourself up. Frankly, even though I got a pass from my ophthalmologist only yesterday during my annual check-up, I would never been able to focus well enough on the actual model held as closely to my eye(s) as your photos show to render a more critical opinion! At that distance, I'm a 'Magoo'!!
OTOH, if you had asked my opinion of your finished item from a normal viewing distance/angle/lighting...you know, standing by your layout, watching the trains go by or burbling at idle..., I guess my reaction would be more like...'Defects? What are you talking about? Looks GREAT to me!'
That would be an interesting 2-part psychological experiment some time. Post this question showing the model, the paint job, the color concerns, the masking job, ...all the irksome 'nits'..., with a photo view in the proportions that a normal viewer would be asked to judge by. Get some opinions thereof.
Then, post as you have here...close-up views, side-by-side comparisons, perfect focus, perfect lighting, etc., blah, blah...and see how the responses compare.
Moi...'Would that I could be that skilled, lucky, whatever when doing a custom color/mask/paint/letter job on a loco/car!'