Q:Will there be any problems loading the original Windows
software that came with my Gateway (new in 2001)onto a new
hard drive?

No problems, but sometimes the software can only installed for a
specific model. I see it couple of times in PowerDVD that comes with
DELL. If it happens, you can edit the file like Custom.ini.

Q.Any suggestions about making sure CMOS (or BIOS?) is set
correctly? Someone cautioned me about this several months
ago when I first got serious about changing the hard drive.

Just load the default setup in BIOS and that it. I think the risk are
in installing HD and connecting the cable, especially the static
electricity .Static electricity can kill the HD contoller board
instantly.
Just do it slowly, and it will be fine.
Also old motherboard (like 440Bx-base board) does not support 128 GB
hard disk, in this case get a promise ultra 100 or 133 card.

Q.Have people found they prefer external hard drives? Are they
easier to hook up?
External is more expensive and slower than internal

You can check whether your HD is faulty by using HD manufacturer
software. There is a software called smartmontools, which reports the
status of HD like spin up time, hour of usage and the staus of
relocation sector etc. This software is quite accurate, try it.

I would recommeded Seagate since it is quiet and has 3-year warranty,
and Western digitial has only 1 year. I dont recommed Maxtor since they
fail frequently.

I think gateway 900 motherboard supoort only IDE, not serial ATA. So
you can only choose IDE hard drive
Also,buy HD in Best buy or circuitcity since they offer rebate, and
they may sell it cheap on black Friday next week.

Q. Should I be concerned about the buffer sizes?
Yes, more is faster and better. Get a 7200rpm and 8MB buffer HD.

Just curious, what error messages you got upon startup?