I specifically breed for high anthocyanin foliage corn and have been doing so off and on for at least 10 years now. Many varieties do have a weird linkage with some unuseful genes where they will will grow only tiiny cobs covered with extra layers of husks. And sometimes the amount of anythocyanin might interfere with the amount of light reaching the chlorophyll, so it's possible that the green corn plants will grow better than purple ones. But based on my observations with other high anthocyanin species i suspect that is mostly just a breeding / selection problem. I've seen purple corn plants grow tall and healthy and produce big ears of corn just the same as green ones. I think it is just a matter of finding / starting with those varieties from the beginning OR doing lots and lots of crosses to break the bad linkages.
I think my purple corn population is finally starting to head in that direction. I did a grow out last year and i didnt see any of the weird husk or growing issues that i've seen in the past. I have a fellow who is growing some out in the nearby town of Longmont, Colorado this summer and he is going to plant some coming this fall / winter in Texas since my population was originally being bred to thrive in early early spring here even with snow. I have plenty of seed i could probably share for your project. But i am also always on the lookout for purple corn varieties with GOOD genetics and that grow large ears. It's important to have more genetic diversity in such a population in my opinion.
It should be noted that i dont breed with flour corn, only flints.
I grew Maiz Morado from peru years ago, but it grew too tall and too long season for it to be much use to me at the time (without selection, which i probably should have done), so that sounds cool that you have a variety that does well here in a temperate climate.
The maternal line is the important one i'm pretty sure. But joseph is right in that you sorta get out what you put in. If you have a line that grows weak or weird then without crossing and crossing it you will still have that problem for awhile. Which is why i'm thinking genetic diversity for such a narrow trait might help.
I'm surprised you have japanese beetles eating your silks. that seems very unusual to me. Are you sure they are not the yellow cucumber / corn root earworm beetles? They are VERY common. They will eat any corn variety. The best way to combat this is to practice crop rotation so they don't gain a foothold in your soil. They will always come back eventually if you stop the crop rotation though.
sadly i don't have many good photos that i can find right now.