Is it a B3 or G0 stepping? I supposed by "all the thermal throttling turned off" you mean features like Speedstep (often called other things depending on bios)? They are not really throttling but a power saving feature. However I think the CPU will throttle down or turn off at the Tjunction or...
Yes, you should definitely remove the old AS5. You can use Isoprophanol, acetone (the one without any form of oil etc.). There are other compounds that can be used too. Check the PDF for instructions.
http://www.arcticsilver.com/pdf/appinstruct/as5/ins_as5_intel_dual_wcap.pdf
I ordered one of those for my Q6600 G0 today. I hope it's as good as I think it is. I've also heard that the included paste is supposed to be pretty good, for some even better than AS5. I just assumed AS5 was much better before but now you start to wonder.
Sure, it's there but if you notice it probably depends on a lot of things like monitor you hade before etc., Good or bad eye sight has nothing to do with it though. Also, you can get used to the ghosting of your specific monitor which makes you almost not notice it unless you think about it.