CPU2 Vcore reading is actually your Vmem, which should be 2.5V. It isn't a bug. It is the way the K7D reports voltage. Vcore1 and Vcore 2 are the same.
Your temps are normal. You can try lowering the Vcore to bring down the temps. Also case airflow is incredibly important with AMD duallies. If your case airflow isn't great, then you can have problems with your temps.
The lower 66 MHz/64 bit PCI slot shares an IRQ with the AGP slot. Usually this isn't a problem, but if your controller is real picky, then it does usually help for it to have it's own IRQ. I've used an LSI SCSI card, and two different Highpoint IDE RAID cards in the lower 66 MHz/64 bit PCI slot, without any problems.
If you want step-by-step help setting up your system, read my sticky in this forum. There is a link in my sig.
There is more info, there, then I care to repeat. I think it will answer most of your questions.