I may have to reinstall windows home server. I have 2 additional hard drives installed. If I reinstall, can just add the additional hard drives with my data to the new install without losing the data?
No. When a drive is added to the storage pool, it automatically gets formatted.
Additionally, the install drive also has a portion of the data partition. Will a new install wipe the whole install drive or can I keep that partition? I have enough room to backup that portion but I'm not sure how.
You want to do a Server Reinstallation (or, if you have a pre-built server from HP/Acer, it's called Server Recovery). It wipes the OS partition, leaving everything else in tact.