I went through the exact same decision and took the 400/5.6, magnificently sharp though it was, off the table because of the lack of IS.
You know my favorite animal.. and it tends to stay on the ground rather than become airborne, therefore IS is a gigantic asset. For airborne critters, I don't find IS very useful, in fact I switch it off because I am usually fighting IS while panning on both axis.
The 300/4 ISL is magnificent.. give it 1/3rd of a stop and sharpness approaches the 'out of the world' feeling that you get only from things like the 60 macro.. which is my reference standard for resolving power. The 60 macro should be an L.. it smacks most L's silly.
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The best part is that the 60 macro is built on plain glass.. no exotics. The only unusual aspect to its construction is the presence of a sub-aperture before the main EMD aperture system - in other words it has a two-stage aperture with two sets of blades instead of just one set.
I would have no hesitation taping the pins to disguise the TC's presence, for both interoperability on my 100-400, and max AF speed on all my other lenses.
