hi @Amir Haq - Taking in to consideration , the amount of money involved ( I dont know for sure , but digging the basement is a huge task ) , I would suggest to talk to neighbors or even just looking at other "duplex" rentals posted in the are a call them .
Another approach which might sound extreme is - talk to an attorney who is well versed , I dont think he would offer a silver bullet , but if you find the right one who specializes ( tricky part is finding some one with good knowledge ) , they would give you some sort of advice. I had a zoning qn on a property in suburbs and talked to three different attorneys as part of their free consultation , and I am sad to say that , even though they mentioned it as one of their expertise , I dont think they have any real world knowledge.
The other qn I have is - I am sure , you had this duplex plan at the time of buying , were you aware of the height issue or were you under the impression that , you would just duplex down and realized after closing .
On a tangent , regarding contractors , I would suggest to stick to individual trades , I understand your rationale for finding that good GC , but I wont waste time . Far less risk and you get to control the project .
Also for tis project , before you look for contractors , I would suggets to look for solution and find contrcators to do that . As these two are different parts . For ex, dont ask a contractor " hey , what should I do to make it legal " . Its open ended
Work with experts and once you find a solution then clearly mention what you need done - for ex " We would like to bring down XYZ wall , dig 6 inch ..and so on "
One more thing , even if you keep getting the same suggestion from various parties , that might be the only option but make sure that if you dig the basement , what other things might or will come up . You need a true third party to advice on this .
Hope it helps