I have a 5.9 12 valve and also looked into the things you mentioned. First, the limiting factor on increasing HP or torque isn't the engine, they can be 'souped' up pretty easy with rather cheap modifications. The limit is, how much can the Allison 4 speed transmission handle? My AT542 would not take much more than my engine can presently put out, so that changed my mind on increasing engine power. Also, if you have a similar transmission to the AT542, it probably has a non-locking torque converter, so any engine braking would not be transferred into the wheels.
I've driven 10% mountain passes out west and found I could do O.K. paying attention to RPM and gear selection. Downshifting to keep the engine in it's best torque range helps on climbing, and downshifting to a lower gear or two actually does help retard speed going down. It's not as positive as an exhaust brake, but it prevents having to ride the brakes or apply so frequently that overheating becomes an issue.