Does the organ have a midi output? If so, you could record tones to .wav files, then use ReaSampler 5000 to pitch shift them with midi input according to the organ key you play.
If the organ doesn't have midi out, feed the organ audio to ReaTune and 'x' the checkbox to generate midi from the pitch. Then the midi output from that can feed RS5000.
Tone Generator isn't really an instrument. More like a test utility.
Do you have a reasonably flat mic? The free REW (Room Eq Wizard) program is a much better tool to measure room resonance freqs.
You'll likely find that trying to use an EQ to compensate for an untreated room will be highly unsatisfying at best. See
http://ethanwiner.com/acoustics.html for a thorough discussion of why.