As far as what will fit. I have a turbo 400 in my 66. It doesn't have the tunnel modified. Maybe you could get the dimensions off that to compare.
I'm kinda surprised at your statement.
TH-400's weren't available from the factory in '66 Chevelles.
Autos were PG's or TH-350's. 400's became available in model year '67.
400's are physically wider on the passenger side (at least), and I know the "hump" had to be opened up on mine to [barely] clear the 400.
To add veracity (?) to my statement, if one needs a floor replacement for a '66, the aftermarket supplies a '67 which is clearanced for a 400.
Getting back to the thread's original subject, I recommend the TH-400 with the Gear Vendors UD/OD. The level of strength can be built into the trans and the GV is good for 2,000 HP outa the box.
Using GV's older (?) analog controller (or their really pricey racing electronics box) and a [unique] shifting procedure will make for a close ratio 5-speed on a full-manual 400. The only additions are a 1st-gear-sensing microswitch and a toggle switch for O.D. in high gear.
Oh, yeah, installing a 4L80 trans guarantees one will have to open up the hump, as the O.D. is in the [fatter] front portion of the trans case.