Hello from a MK1.5 owner and a question about water in the boot + engine knocking noise

Dear all

Hi!! I am a Ford Focus owner. 

I recently owned a Y reg Focus MK1 which I had lovingly for 10 years after buying it for £1,300. The indicators stopped cancelling, the AC stopped working and the central locking didn't work. But it was a great car to drive and got me from A-B. Unfortunately a few months ago I sent it to car heaven by driving it mistakenly into a concrete wall.

However my love the Focus was not diminished and I have got myself an '03 plate MK1.5 with 50,000 miles.

Everything is going well however a couple of niggling issues:

1. Water in the boot. I had a look and there is a lot of it coming in when it rains, to the fact that the spare tyre well is like a pond. I stripped everything out and the water seems to be collecting in the area circled in red within the frame. I thought it might be the gaskets from the rear lights, but I would have expected it to come on the outside and not within the frame where the water is collecting. Anyone else had similar issues in the same area?

2. When I am stopped at traffic lights in neutral I can hear a knocking noise from the engine. If I push the clutch down I don't hear it. Interestingly if I engage neutral before coming to a stop, once I am stopped I don't hear a knocking sound. My initial thoughts is that it might be the clutch bearing? If so can I assume it is not an issue and when my clutch goes I get it replaced then.

Many thanks