caps lock + hjkl requires your left pinky every time you want to move the cursor. This may very well induce RSI because "using the arrow keys" is something that we tend to do all the time.
I'm using the key physically at the left of the space bar (I don't like talking about the 'name' of the key because it's very keyboard-dependent) as the modifier which allows me to move the cursor. And I move the cursor using modifier+ijkl (for ijkl reproduces the inverted T arrow cluster, not unlike how gamers like to use WASD or ESDF). I do hit the modifier using my left thumb, which is a finger much stronger than the pinky (and, arguably, such a setup is less RSI inducing).
Regarding covering the arrow keys and numpad with a mouse platform: many people opt for for a "TKL" (no numpad) or even 60% keyboard (no numpad, no arrow cluster) and typically those 60% keyboards have the benefit of coming with quality switches (also arguably less RSI inducing).
If you want to see what others are doing, two great sites are geekhack.org and deskthority.net.
FWIW I use a 60% keyboard which has CTRL at the correct place (i.e. where CAPS-LOCK is on keyboards which have a caps-lock): an HHKB Pro 2 (using the amazing Topre switches)... Which doesn't even have a CAPS-LOCK key.
Note that lately there seem to be a regain in interest in alternate setups and alternate mappings: for example the "SpaceFN" layout uses the space bar as an additional modifier (when it is held down) and ijkl to move the cursor around (once again: ijkl and not vim's hjkl and a strong finger, the thumb, to press the modifier).
Regarding remapping and "feeling completely lost" on other OSes: if you want to not have to remap your keyboard on Windows / OS X / Linux etc. you may want to buy a keyboard which has a programmable controller: your setup then works the way you want on any computer.