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Am I supposed to make the partitions manually then use the builder kernel to populate the filesystem?

No, the builder is the thing that is supposed to do *all* of the partitioning, formatting, and testing for you. The manual partitioning is only if the builder fails for some reason.

Then after the builder is done, you can put the version 2.0 player firmware onto the player via the .upgrade file.

Are you using the bigdisk builder, or the one from empeg.com?

If you're using the one from empeg.com, one of those files is known to be corrupt, use Mark's bigdisk builders from the drive upgrade guide instead.

Are you using a USB-to-Serial adapter instead of a real serial port?

If you're using a USB-to-Serial adapter, that might be the culprit. Even if it works OK for terminal programs, it might screw up when running the .Upgrade files. See if you can find a friend with Windows and a proper serial port.
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Tony Fabris