Does anyone know how Jeep squeezed the 9 extra ponies out of the 99+ 4.0L?

Well I guess that 100 years of automotive engineering must be wrong. Ask a gen 2 hemi owner what happens when when they go to 36 degrees total timing.... at 32 it will run on 91 at 36 it is blowing holes in pistons

does octane at some point above 91 allow them to run 36 degrees?
 
as to the original question - here's my guess at what probably happened to get that extra 9 hp.

1. They made some design changes like the manifold, port shape, probably some slight cam changes, probably some tweaking of coolant passages to more precisely control temperature where it's particularly important, and a tune to go along with it, all to improve emissions.
2. after the changes they made, they did easily enough dyno testing on enough engines to get statistically reliable performance numbers.
3. the new peak hp on average was up by 9, completely unintentionally. Perhaps something about the flow pattern in the combustion chamber allowed a bit more aggressive timing. Maybe the better emissions allowed a slightly richer mixture at WOT @ the peak hp RPM. Maybe the guy that did the tune was just a little better at his job than the guy that had done the last one. Maybe they did more break-in before the dyno test to let the rings seat in. We'll never know, because it's not likely one thing that made the difference, but rather the whole picture.
 
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Octane has nothing to do with it. The heat and late explosion is what burns the hole in the piston. The definition of octane rating is as follows...
An octane rating, or octane number, is a standard measure of the performance of an engine or aviation gasoline. The higher the octane number, the more compression the fuel can withstand before detonating (igniting).

So, unless you've done something to change compression ratio (pistons, head, or forced induction)a higher octane rating will gain you nothing.

Wrong in both theory and application. You understand little bits and pieces but not the whole thing.

Here:

And that guy has a German accent so you know he knows what he's talking about.
 
Just to clear this up...Timing will not ever require a change in fuel octane. Only engine compression ratio and elevation change will require different octane requirements. Pre-ignition and detonation are two different things caused by different things. Ever notice that in low elevations at the pump your low octane fuel will be higher than even the premium octane sometimes in high elevations? 86 octane is common at high elevation and 89 is about as low as you'll find at low elevations.

That is a gross oversimplification. There are too many variables. Compression ratio is a piece of the puzzle, but IVC also plays a big role in dynamic compression and fuel requirements.
 
Russ Pottenger is the AMC/Jeep I6 stroker guru out in Cali. He can get you HS's in 1.6, 1.65, and 1.7's. They make adjustable sets as well.