First of all HAJIMEMASITE, welcome to the BB!!
I would check if the 1600 engine the shop is offering is original to the car (it should have AR00502 XXXXX stamped right by the mechanical fuel pump on the right side of the engine block). If it is indeed 502 type engine, I would keep that engine (meaning keep it in your hands, not necessarily in the car) just in case you wish to make your car true to its original status. Considering rarity of the car, I think having the correct engine available is very important. Now, knowing how it is like to drive an carburated Alfa in Japan, I would recommend the 1750 because of its characteristic. It's torquey enough, yet it also loves to be revved (compared to the 2000) and I like it very much. On the other hand if you live in rural area and do not have to worry about cars around you, 1300 is very fun to drive and make you feel that you are driving really fast without risking your driver's license. The 1600 as you may have guessed, is somewhere in between these two engines, but more importantly this is THE stock engine for your GTC. After all, it's matter of preference so if it's possible at all, I would drive different Alfas w/ different engine (1300, 1600 and 1800) and see which one suits you best. If I were to pick one, it would be the original 1600 though.
Hope this helps,