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Remapping is very easy. Many resources recommend the xmodmap command, but I've had much more success on recent distros by setting xkbmap options in the Xorg config.

A big list of possible rules are located at /usr/share/X11/xkb/rules/base.lst

Changing alt+tab to ctrl+tab is easy with most window managers.

(I find the alt/command physical key much more ergonomic than the physical control key.)

You tough it out like a grown adult hacker, and don't whine about it during the 2-3 days it might give you trouble (cursing is fine, and in fact encouraged).

I've used OS X since it was called 'System 6,' and used GNU/Linux on and off for years, so it's generally just a few days of 'dammit.... Dammit. Dammit.' and then I'm fine.