First off congrats on your new purchase!
On to your questions..
Can I use a Sata drive run from a PCI Sata controller card as the boot drive?
Yes you can. I am booted from a SATA drive on a PCI card as I type this. For your needs I recommend the 4 channel PCI SATA card FirmTek sells.
Will the power supply be up to running 6 hard drives inside? (4 in standard locations and one in each 5.25 bay)
Yes. The Dual 867 has a 400 Watt PSU and can easily handle 6 drives. All modern drives consume around 12-15 Watts so even 6 would only be around 75-90 Watts. Unless you want to use more than one SATA PCI card you will have to make 2 of the drives PATA.
Are there any perennial issues with this model I should look out for?
The MDD is the most troublesome G4 tower but keep in mind the repair/recall on these was only for about 6% of them which is very good compared to G5 towers that range from 11-32% of systems needing repair. I have owned 2 MDD in the past and based on that and other research I have done the Dual 867MHz is the most rock solid of them all. The MDD's main issues were fan noise and some of the PSU's die after just a few years. There are a few guides around though on how to rig a standard 24 pin ATX PSU to power an MDD.
Considering it's about 8 years old now and still running you definitely have a good one.
I want to give it a good going over before I get it up and running. I was going to clean and reapply Arctic silver to the CPU/heatsink interface, upgrade to 2Gb RAM, replace the rather noisy fan with a higher CFM quieter version and anything else you guys can recommend
On to your questions..
Can I use a Sata drive run from a PCI Sata controller card as the boot drive?
Yes you can. I am booted from a SATA drive on a PCI card as I type this. For your needs I recommend the 4 channel PCI SATA card FirmTek sells.
Will the power supply be up to running 6 hard drives inside? (4 in standard locations and one in each 5.25 bay)
Yes. The Dual 867 has a 400 Watt PSU and can easily handle 6 drives. All modern drives consume around 12-15 Watts so even 6 would only be around 75-90 Watts. Unless you want to use more than one SATA PCI card you will have to make 2 of the drives PATA.
Are there any perennial issues with this model I should look out for?
The MDD is the most troublesome G4 tower but keep in mind the repair/recall on these was only for about 6% of them which is very good compared to G5 towers that range from 11-32% of systems needing repair. I have owned 2 MDD in the past and based on that and other research I have done the Dual 867MHz is the most rock solid of them all. The MDD's main issues were fan noise and some of the PSU's die after just a few years. There are a few guides around though on how to rig a standard 24 pin ATX PSU to power an MDD.
Considering it's about 8 years old now and still running you definitely have a good one.
I want to give it a good going over before I get it up and running. I was going to clean and reapply Arctic silver to the CPU/heatsink interface, upgrade to 2Gb RAM, replace the rather noisy fan with a higher CFM quieter version and anything else you guys can recommend