Allison shifting funny

[The Lurch]

On a '02 4500 D/A truck, the transmission has started to do something funny. When it gets warmed up, it almost acts like it is in a limp mode. It will continue to shift, but you have to let way off the throttle. Fluid level seems fine, and there doesn't appear to be any electrical components out of place.
One thing I did notice is that on the passenger side exhaust manifold, there is a bolt completely missing, which makes the motor sound like a bad tuned gas motor. Could that lack of compression mess up the tranny?

[DmaxMaverick]

In nearly every case of delayed shift I've seen has been a need for a filter replacement. A plugged up spin-on filter will reduce the fluid volume (and pressure) needed at higher RPM's. These filters are pretty efficient, but small. If it's never been changed, that would be my bet. If it has been changed recently, try a full service and new filter before throwing $$ at it. An exhaust leak won't cause poor tranny performance, but low power from the leak can. Reduced expected power at a shift point will delay the shift. More pedal input for the same power = later shift. Meaning, it's not a tranny problem, but a power issue, causing delayed shifts. If you have an exhaust leak bad enough to sound loud and like a bad tuned gasser, it may be significant enough to reduce boost pressure, which translates into less power. These engines are assembled w/o exhaust gaskets, but gaskets can be had. You may need them.