Picked up the car today and everything seems good. They could not re-calibrate the speedometer. They said that they would have to reset to factory defaults so since I have a Bama tuner I will do it myself. As far as I can tell the speed is only off about 2 mph when matched with my GPS. I may just let it be but with my OCD I will have to do it myself anyway. At 60 MPH in 6th gear I was turning about 1,700 rpm and averaged about 27 mpg coming home on the highway. We will see how all of it works out. Since it was raining I didn't give it much gas.
Not sure which Bama tuner you have, but for my '14 V6, I have the X4/SF4, purchased from AM which includes 'Free tunes for life'. This allows user selection for some criteria, such as top speed limiter, tire size (in 'revolutions per mile') and final gearing, etc.. From my experience, with this particular tuner, the last tuner files provided (by AM) were incorrect (255/40R19 tires' diameter of 27.0" calculated to about 746 RPM and my tuner file was set at ~790, resulting in speedo indicating about 11MPH lower than actual); despite the advertised ability for resetting this by the user, apparently the user selections (745 RPM) would NOT override the tuner file and I had to go back to AM to have a new file sent with the correct tire RPMs. I just installed the new tune files yesterday and have not driven it since, so I'm not yet sure that this has resolved the issue. Bottom line of the cautionary tale, if you're not able to correct the speedo error w/ your tuner by adjusting the user-defined criteria, you may have to go back and request an updated file (assuming that this service is available to you by your seller).
Also (and likely too late), I too have parts on hand for a 3.13 > 3.73 gear sway for mine. While it was a few years back, the gear change on my '66 at my local transmission shop ran about $450 for labor only (plus parts, which I ordered/provided). While I know it varies from one dealer to another, some just do NOT like to deal with installation of non-stock (and particularly non-FoMoCo aftermarket parts). As an example, my local Ford dealer has turned me away, refusing to install items such as a non-Ford rear deck lid spoiler (neither they nor I wanted to drill through the trunk) and
Eibach progressive-rate lowering springs (I was told that they "didn't have the
right spring compressor" ?!?). While other Ford dealers may be more apt to work on non-OEM parts' installs, mine seem less willing to do so. I don't have any heartache with this, as generally speaking, their shop rate is MUCH higher that other competent alternatives.