Sounds like a lot of work, I would personally not worry about it. It's easy enough to get rid of the sunroof with a sheet of metal. I wouldn't want to go through the trouble of cutting off the entire roof and sectioning in the non-sunroof section. To do that right would be a lot of work-- more than just a simple panel welded in place of the stock one. Lots of E30 racer guys around here do that. Other guys just gut the roof of the sunroof stuff and make simple brackets to fasten the bare sunroof panel in the hole and seal it on the top.
^My opinion.
^My opinion.

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