I know this question is 9 years old, but still hanging in there.
I've cracked this problem over a span of 15 years.
I've gradually perfected a very lightly customized keyboard layout over that time, that doesn't use pinky for CTRL. Initially I did it only so that I could have roughly the same keys for the same common functions, across Windows, MacOS with Apple keyboard, and Linux. (And any of the previous on any keyboard layout, e.g. Apple keyboard on Windows.)
The optimal way to accomplish this, is in part, to remap the CTRL function to the left Alt. Then, you activate CTRL with your thumb. Easy-peasy.
And Alt now occupies what was formerly CTRL, both left and right. Often times to activate that, I find it easier to just lift my whole hand - left or right - and press it with my THUMB, with brute-force like a monkey, and then return my hand to home row. This sound crazy actually writing it out, but it works. And this, in spite of the fact that 1) I have long fingers, 2) I'm a musician with strong flexible fingers, 3) I'm a touch-typist who can type 100 wpm if I put my mind to it. It's just automatic, fast, and it works.
For Windows on a standard PC keyboard, I remap:
- Left ALT = Left CTRL
- Left Windows = Context Menu
- Left CTRL = Left ALT
- Right ALT = Right Windows
- Right Windows = Right ALT
- Right CTRL = Right Alt
I do this on all machines, Windows or Linux. For Windows I use an ancient utility called KeyTweak. It remaps things in the registry and requires a reboot, so it doesn't matter that it's an ancient 32-bit program; and it works on any keyboard no matter the scancodes or funky layout. For Linux, I use a custom script that, surprisingly, took a few years of debugging to work reliably every time. It modifies XWindow keyboard mapping and has to be run after every reboot.
Hope this helps.