Hey Andrew,
Like I've said before, I'm no Studer expert.
The low freq. rumble you hear could very well be mechanical rather than electrical. One way to narrow this down is the try your experiment again with the tape running at different speeds. If the rumble changes frequency, it's mechanical. If not, it's probably electrical. If it seems to be mechanical, try listening to your machine with a stethoscope particularly around the capstan. It could be the bearing.
Other things you should do is clean and check all the rolling surfaces the tape passes over. A little bit of play in a bearing will cause cogging and it amazing how these little things that seem very isolated from the heads will be audible. I doubt if the noises you're hearing will be solved by demag-ing but if you haven't done it in a while, go ahead and do that too. You really should have all the cleaning/demag. done before you use a test tape. They need to be as accurate as possible to be useful and any oxide build up or residual magnetization will damage it.
One word of warning. If the high frequency fluctuations are coming from the same channel as you replaced (if the problem doesn't follow the card) avoid recording until you have a better idea what's going on. It may be something upstream of that card that whacked out the original.
I'll leave it at that and let the real Studer guys take over.
Oops, just remembered, check the connectors (molex) to be sure they're nice and clean. A pin that has a bad connection over time will get dull looking and corroded.