> The right Ctrl key is in a very uncomfortable position whether I press it with my pinky or with the base of my hand

When I used a traditional keyboard I rebound ctrl to be next to space so I could easily hit it with my thumb so the layout was like:

    [super][alt][ctrl][----space----][ctrl][alt][super]

But now I use a split keyboard(Kinesis Advantage) with ctrl/alt/super in thumb clusters that make hitting those modifiers really easy.