I've seen loads of cossies running without, so im guessing you'll be fine. Same goes with the RST's though, loads of them go without too. Im now guessing its down to your own piece of mind really.

The cover i have won't fit properly since converting over to ZVH... I dont know why, but it just wont! On the CVH it was a struggle getting the bolt closest the bulkhead to go in line, but eventually it went in. So maybe thats just it again, not sure.

The bolts that come with the clear perspex cover are longer, yes. You should have had some sent with it when you bought it, but if not, and as said, just give the guy an email and im sure he will send some out. The rubber that is being mentioned is the rubber seal off the original cambelt cover. Just take it off the original cover and put on the new cover - simple job