Whs /\ Cut out the modified bits, weld in flat Steel, then make a template from the glass to mark out where to cut. From memory, I think you need to add 5mm all round the glass to allow for the rubber. (Check that measurement yourself though, don't trust my memory lol )
That would rot out mega-quick if you left it. Whoever did that was not very good. Makes my welding look brilliant. If it desperately needs rain proofing for now, I would get some duct tape and tape over between the glass surface and good paintwork on the body. Then as @Dubs says, fit enough metal and cut out the right size hole the second time.