That is no task for the weary and is very involved.
I had made some block out plates just like that for mine to get me through the rainy season until I could tear into mine.
It slowed down the leaks but didn't eliminate them and it sucked not having the fresh air anymore. There are a ton of threads on the cowl repair, a few different opinions on how to do it. But what ever method you choose, you will need a cutting wheel, welder, some sheet metal, metal working capability and patience. And patience. Did I mention patience? Also, take lots of pics before you start and as you go for reference.
I have some photos on my garage page of how mine went, if you want to check it out and I know that Q has a pretty cool instructional vid that walks you through the repair.