So far I have found four separate areas in which water can (and has) entered the boot area. Hopefully, I have plugged all the holes now, and this information should help everyone else find where the boot is leaking from.
Fixing Boot Leak in 1996 Civic Coupe
First (and most obvious) is the sunroof drain hose. They are clear plastic tubes running down each side and the slot into rubber linkages which allow the water to drain outside the car. There is one each side of the car, and one of mine was draining into the boot.
Fixing Boot Leak in 1996 Civic Coupe
Second is the rubber boot seal. Mine was loose and not sealing properly so i sealed it with silicone sealant all round.
Thirdly, does your bumper look like this:
Fixing Boot Leak in 1996 Civic Coupe
Fixing Boot Leak in 1996 Civic Coupe
If so, it may be because the clip holding the bumper on may be broken, and you may have a leak as it isn't sealing properly. I just covered the whole thing in sealant (and hope for the best!)
Fixing Boot Leak in 1996 Civic Coupe
Fixing Boot Leak in 1996 Civic Coupe
Lastly, I found that water was getting in through a leaky join near the filler cap. Again I filled it with sealant and will hope for the best. The final pic shows the inside of the filler cap and the wheel arch.
This one was a bit messy, but I will clean it up later.
I used Unibond roof and gutter sealant for this, though any silicone should be OK. Hope this helps everyone who has a leak. If I find anymore I will update this page.
