how to use xmodmap in ~/.xinitrc
 

It is my understanding that X is mangling my keymap that is loaded from .xinitrc because of hotplugging and xkb. I only use fvwm/startx, what can I do?

just set up a file with the things/commands you want xmodmap to do (man page has a fine example of swapping ctrl and capslock) and then in your ~/.xinitrc file just add
xmodmap /path/to/that/file

that's what I've done. the problem is when I start X. The new map is not loaded. I have to manually run xmodmap $HOME/.xmodmap. One solution I found through googling was to put the xmodmap command into .xinitrc twice. it works, but I haven't found a better way

that is so bizarre I've never had to run it more than once in my .xinitrc, wonder if your session manager is doing so modmap on it's own. Do you just put them back to back or do you have other stuff in between the two xmodmap calls?