That was really hard to do, but mostly because it was like this before:

But mk2's are half done for you! I would get some filler with a bit of flex in it.. such as this

If you need to put a fair bit in, mix it with normal fibreglass filler for strength.
Imo the most time consuming part is getting all the old rubber sealant off, so a good blowtorch is a must! When doing the Ibiza bay I just made a template from card and tried to make it all from as little pieces as possible. Welding a little at a time saves a lot of warping of the metal and a lot more filler and effort later on. I will try and dig up an old build thread of a nice bay.