"Is there a way to ultimately tell what your sub is tuned to, so that you can put the high pass filter at the correct frequency?"
without any gear, you can run some test tones and watch the cone motion. at tuning, the cone will move little. above and below it will be moving much more.
"Should your HPF be set at the same frequency as your tuning frequency?"
it doesn't have to be exact. at tuning or a little lower is common.
"Given that price was the same for both processes, would you go with the more powerful ep 4000 using my process or the inuke?"
they actually output about the same real power, approximately 2000 +/- watts from both amps. with a 4 ohm driver on each channel, you'll get around 650 +/- watts or so into each driver.