Hi sallycinnamon
As dinx said lets see pic's of the car. Also at the mileage of your cab, its just running in really..
Regarding leak in the hood - this info might help you. (Price is about right for ne w hood, make sure they replace the cables as well for hood, this is key..)
Have you checked the rubbers on the doors are 100% ok, as I've had water come through from them before near bottom. Also the front arch's where the body kick is someones water gets through between bodykick and main body and holds there and then rots body and leaks inside right near carpet.
If you really want to test out the roof - get hose pipe and turn on - doesn't need to be blasting and put over the front door roof area about 4 inchs from edge and go back and forth to cover the whole window length for about 1 minute and watch to see if the water is leaking into the car - usually the water comes in from the front door seal or at back of door where top rubbers from roof area are not up against each other properly - this is due to wear. - I had this on my current cab and replaced rubbers and hood all went away..
GPC provide all cab rubbers - but expensive...
http://www.gpcvwaudi.com I find the following company A1 for hoods -
http://www.autohoods.co.uk/contact.htm - they will come out to you and fit new hood..
On the alarm, I would get a new one and I find TOADs are properly one of the best around these days and they are priced really well. I have a I606 Toad installed on my Mk1 cab and its excellent, even have the pager option as well, so if the alarm goes off I get paged