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In my boot sectors BPB, how am I supposed to know what reasonable values are for things like BPB_SecPerClus or BPB_RsvdSecCnt? All I'm going to be using the file system for is my second stage and kernel.

Also, what do I need to read off the floppy and interpret to find my files? I understand there is a reserved region for the boot sector, a FAT region, a root directory region, and a data section. What has what in it (besides the obvious data section)? What format do the entries have?

I read the FAQ and some of the FAT spec but I'm kind of confused here...

Go here and get "bootprog.zip" great program in nasm, which is well commented and will give you all the info you need.
http://alexfru.chat.ru/epm.html

\\\\||////
(@@)
ASHLEY4.

My bootloader. May be useful,(its quite easy to read and understand).
get it here

the FAT file system specification from Microsoft?

Hint: google for "FAT file system specification microsoft" and take the .doc link from microsoft.com.