fine tuning speaker placement

I would not sit 3 feet from the rear wall. I suspect those tiny variations you are seeing are from comb filtering from reflections from the rear wall.

Try sitting 6 feet from the back wall.

Consider that you are sitting way too far away from your speakers. Assuming that you have them firing them down length of the room you have them about 7'4" apart and your head(chair) is about 14' away. That will muddy up the mid's
and greatly reduce all aspects of imaging, especially sharpness.

I prefer an equalateral set up, but no more than 11 to 10 ration (speaker distance to chair/speaker distance to speaker).

Re the HF suck out: 1) Suck out if narrow enuf, say 1/4 octave or less will hardly be audible but if so it will be minimal sonically. You can not correct it by adding room acoustic treatments, but as you mentioned altering the toe in can change the FR as the horizontal dispersion of speakers is usually uneven and finding the magical position is usually best done by ear.

Assuming that your speakers are presently pointed straight ahead, you might find that toeing them in will reduce reflections from the side walls which will allow you to increase the spread between your speakers. In fact if you were willing to increase toe in until the axis crossed at or in front of your listening position, you might easly increase the spread to 9 to 10 ft without the lower octave FR changing much at all.

Re mic position I always use a hand held SPL meter with the mic pointed straight ahead and I position the mic where my head would be. I just chart everything on a graph for reference. I don't know of a reliable visual aid for the entire FR outside of some equalizers. BTW, FWIW, the Velodyne auto equalizer has a +/- resolution of 3db. So much for flat bass integration. Don't know how accurate their graph is. :-)

Only fools make recommendations in the blind, especially those who have never heard your speakers in your room, so here goes. Move your speakers out into the room to 66", move your listening chair out into the room to 66" and now move your speakers sideways until they are 2 ft from the side walls and cross the axis slightly ahead of you head's position while sitting in the chair. Don't measure anything, just put on a great disc and see how it sounds! Work from there, bass FR first and sound stage next.

Enjoy........(Great speaker set up is much more of an emperical process done by ear over a long period of time once you have some initial set up's via Rives Cara program, Cardas, what ever. They are at their best only starting points which are as often as not dissapointing.)

Frequency variation with small changes in position is normal in the high frequencies. If all you have is the 3.6 kHz dip, you're doing very well. The front and side wall spacing you've calculated should be working nicely for you. I doubt half way into the room will improve much. It will change your measurements, but will it improve? Only your ears can tell you that.

Unless I've done my math wrong, you're sitting 10' 8" from the speakers. You might try moving your listening position up 1 or 2 feet from the back wall (2' would put you at about the equilateral triangle position). This will increase the direct to reflected sound ratio and should improve both transients and clarity—not dramatically, but noticeably. You can experiment with toe-in from there. Sometimes a very slight toe-in is all it takes. Give yourself plenty of listening time with many different recordings. It may take some days or weeks before you get it settled.

By moving either the speakers into the room or the listening chair into the room, there will be a 10db suckout at 40-50Hz. However, the midrange and depth perception are better.

If I move to speakers with 13 inch woofers, would that allow me to move the speakers further into the room and fill in the 40-50Hz area?

I agree with all the trial and error suggestions above. I need to do the same with my Avalon Indras, which I recently purchased. If you do want to visualize your results though, and have a computer available, consider purchasing "TrueRTA" on the web and a behringer mic made for calibration (around $60 from Musician's Friend). You can use it to continuously generate pink noise and view your frequency response.