I should start off by saying I am a total PT3 newb and apologize if I'm asking something that has been covered before. I've done some research on this problem and so far nothing has come up.

So...

My Auto Import won't import a very large % of hands and seems to stall whenever it gets to a certain point a little over half a year ago. However, the Manual Import works just fine, and I now have all of my hands up to 3 hours ago imported. Here are my questions: 1) Can I somehow tell Auto Import to skip trying to import old hands and go straight to importing new hands? 2) Is there a way to get the HUD Display without having Auto Import turned on?

I'd really like to avoid having to manually import all of my hands, and obv I want use of the HUD whenever I play. Any help would be much appreciated, thanks

1. Auto Import is not designed to import large numbers of hand histories already in place - you did the right thing using Manual Import. However, manual import doesn't move the files. I'm guessing that you installed Build 5.2 because the new version (Beta 30.9) has a Setup Wizard which would have set everything up for you - imported and moved the old files.
What you need to do now is to move the hand history files to your 'Processed' folder - see the Tutorial - Preventing Duplicates.

2. No, the HUD is triggered by the auto import. Auto Import uses very little resources relative to the HUD anyway, so once you've sorted out (1) you'll be fine.