The easy way to do it is to connect a CDROM drive onto your platform and then just install any linux you want normally from the CD-ROM. PC-104 is just a "physical" interface, if you take a look to the buses, you'll find ISA and PCI signals, so software doesn't care about it.
If for any reason, you don't want to make a standard install, you can boot your PC104 system from a live-cd a "grub-install" will do the job.
Another way is to mount your flashdisk into an USB to IDE adapter and then make "grub-install" from your development plateform.
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