Like the switch, you have an option here. You may chose to simply reattach the lid with no modifications. Be aware that eventually the plastic on the stock lid will begin to melt and droop.
If you decide to go ahead and tackle the problem now you will need to disassemble the lid. The lids are usually screwed together or snapped together.
Pull out the trusty tin snips and cut a piece of tin to cover the area the window once covered. Use some spare screws to attach the tin to the lid.
Reattach the cabinet to the chassis now. You will need to “eyeball” the positioning of the lid so you know where to attach the hinges. With the cabinet in place, attach the hinges to both the cabinet and the lid.
You should now have the cabinet attached to the chassis with the lid attached. The lid can either be the custom lid or the stock lid.