Which version of LinuxCNC are you using? If it's the base v2.7 and the mchine is a vanilla design then most if not all of the configuration can be done from the setup wizards rather than write the .hal and .ini files by hand. I never once looked at those files until I upgraded to v2.8. You can certainly create most of what you need fom there and then edit as required later.

Re the parallel port: I know there are issues regarding finding an add-on card rather than a built-in port but cannot remeber what the answer is! It has been talked about on the forum before.