They're in a little far, but I wouldn't sweat it. Certainly punching them out and going around again isn't too good for a press fit either. Ride it.
As for the paint...looks good to me. You'll never see a lot of that damage when parts are hung. Ride It.
IIRC this is done for some cranksets... my Rascal had this too, it had an XTR M900 crankset installed and the bearing on the drive side had to be "offset" (or is that "inset"??) a few mm into the shell. I looked it up in the KLEIN manual and this was correct. But because I have an XT crankset installed I had to take them out and put in a longer spindle (125mm as to 108mm before) and align the bearings with the shell.
And yeah, go ride it... you can always get a respray done when the paint goes bad or faints too much
Oh man, this isn't happening... it only thinks it's happening - Kevin Flynn
1990 KLEIN Rascal - 1992 Specialized Stumpjumper FS - 1992 Specialized S-Works Carbon - 1992 GT Xizang LE