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It has been a number of years since I had a 1D Mark II and 100-400 at the same time, but, about 7 or 8 years ago, I used that combination regularly. While I can't recall an exact number of shots that I got with combination out of a battery charge, I'm sure it was more than a few hundred, and I kept the IS on at all times.
How old is the battery? If it is one that is of a vintage from around the time the 1D Mark II was a current model, it would be pretty old by now, and it could well be the case that its performance has degraded significantly with age. If you haven't tried reconditioning (or whatever that process for the 1D Mark II was called) the battery, you might try doing that. The process, I believe, drains the battery completely and then charges it. While it might take some time on the charger to do so, it should give the battery the best charge that it is capable of having at its age.
My experience with all batteries on all bodies and with several different IS lenses is that, while I'm sure IS decreases the number of shots I can get per charge, that decrease isn't dramatic. One of the major factors that I've seen that reduces the number of shots per charge is use of the LCD. On my cameras, I have auto review turned off completely, and I usually don't do a lot of chimping. Also, if I'm shooting something that requires me to wait patiently for long periods of time before shooting and if, while waiting, I'm intermittently focusing on the subject for a few seconds at a time and not actually shooting when I'm anticipating possibly getting a chance to shoot the action I was looking for, I'll see the battery drain faster because it is using power to focus (and spin up the IS) without any shots actually being taken.