Thanks for all your help. I apologise for the delay in replying, I have several hats to wear at the moment.
I am using RU5, but the 'all features' package size is still only 73Mb. I currently have all the network threat protection policies disabled, but even when I briefly enabled them to create another package it didn't make much difference to the size. Should I be worried?
Just to make sure I'm understanding this correctly, if I delete the auto-created AD group, all my clients will automatically be moved to the default folder? Then I just move them to the new structure I've created? I'm a bit worried that they'll be orphaned and I'll be creating more work for myself. All my servers are in this structure and I can't afford the downtime\manpower needed to correct any mistakes. I'm sure you all understand.
The extra policies are a pain, but I can live with them. Like you say, I don't need to use them.
If I can move my clients to make them more manageable then I won't need to reinstall SEPM, thankfully! But thanks for the tips.
Gill