Elliot Naess this is for you!
You have spoken about manual transmission and there was discussion about shifters. I too was looking at manual transmission for my 5.9 12valve cummins. Eaton/fuller seven speeds, and I would expect the same on the other transmissions, they make "shifter relocation" parts. Seems that if you tried all the different variations you have more than a hundred permutations. If you ever go this route, I think you will be able to move a shifter to good usable location with bolt on parts from the transmission manufacturer. This also means you might be able to find what you want in a truck salvage yard.
I am sticking with the 12 valve 5.9 for now. I can put 400 hp and 800 ft/lbs of torque with out doing anything to the inside of the motor.
Fuel injector pump modifications, fuel injectors, and turbo modifications are items to get to that range.
5.9 engine rpm speeds are good up to about 3700 rpm. Apparently 4000rpm to 4200 rpm is a harmonic vibration area that can destroy an engine very quickly. move past this point, and you will see racing 5.9 in the 5,000 rpm range and higher.
with stock head bolts, keep boost pressures to about 30 psi or so. You can lower exhaust gas temps if you add an intercooler if you dont have one already.
Been doing lots of talking to big name people in the hopped up dodge 5.9 world. safe to use most of stock stuff up to about 300 hp. That means mostly fuel upgrades to get more fuel into the motor.
300 to 400hp some work to the turbo is needed.
a 400 hp motor would probably look some thing like this.
injectors, governor spring change, "fuel plate", tuning of parts on the fuel injector pump, change of turbo, 4" exhaust, change valve springs. big honking air cleaner -BHAC, gages advised, exhaust gas temperature -EGT, fuel pressure into the pump, advised to me 15 psi is absolute minimum, any less and you are losing power. and boost gage. up to 30 psi with stock head bolts, up to around 40 then might need to fire ring cylinder head. oh and a change to injection timing.
as a general rule, bigger turbos mean more air and cooler egt on heavy pulls.
You can do a p pump conversion to a 24 valve. you get a little more power using 24 valve for the same amount of fuel used in a 12 valve. The short block on a 24 valve is the same.... almost. Word is stay away from 24 v blocks with 53 cast into the side of the block.
Look for something called KDP or killer dowel pin. This is a known problem point in a cummins 5.9. Pin falls out and can get caught in the gears and destroy the engine.
anybody feel free to chime in if they feel I am off base.