I am coming into this conversation a long time after the middle of the show so I don't know how my comments will fit in with the rest of the discussion.
First off, I would not turn that engine faster than 2600 RPM except for once in a blue moon. It wasn't designed or built to spin much faster than that. About the only thing you do when you spin it much faster is you use more fuel faster. The torque and HP start going the wrong direction after about 2500 RPM.
Second, in regards to using a brownie, I think that is a very elegant way in which to get OD gears. The reason you don't see them that often is most people can't shift an automatic transmission properly. To try and train fleet drivers how to shift an auxiliary transmission is a non-starter in most bus fleets. Besides, since most school buses spend more than 95% of their service life at speeds less than 35 MPH the need for a lot of gears is just not worth the extra $$$. I am glad you didn't try to mount a 2-speed rear end. The gearing in all of those were geared for speeds from back in the day and not for the highways of today. You would have ended up with slow and slower.
Third, putting a turbo on your engine is a GREAT idea. Going with the Banks kit even better. When Ford started offering that engine with a turbo Banks was the OEM parts vendor to Ford. Without increasing the amount of HP it won't matter how many gears you have. It takes a certain amount of HP and torque to get a vehicle down the road and up the hills. You could double the number of gears you have and it won't make a bit of difference on how fast you get up the hill if you don't increase the HP and torque.
Fourth, now that you are going to be putting out more HP and torque you are going to have to manage the extra heat that extra HP and torque are going to create. On your trip east you did it at a time of the year where getting heat out of the heaters is a big issue and not getting rid of excess heat. On your next trip if it is going to be done on a hot summer day you stand a great risk of burning your engine up. There have been hundreds of vehicles burn their engines up heading west on I-80 in WY. The grade west of Cheyenne isn't very much for more than 100 miles but it is consistently on the upgrade. Because it is so gradual most people don't realize how much work is being done under the hood. With ambient temperatures well in excess of 80* you will discover how well your cooling system works and where you can have your foot on the throttle to prevent melting it down due to excessive exhaust temperatures.
I know I would not want to swap an Allison for any stick shift simply because I live in western WA where you are more likely to get stuck in traffic trying to go through Seattle/Tacoma or Portland than trying to go through Los Angeles. Letting Allison run the clutch is much preferred to letting my gimpy left knee run the clutch.
I am glad you are making your conversion uniquely yours. That is what is so fun and different about conversions--there are no two alike.
Good luck and keep us posted as to your progress.