1990 Honda Civic never came with a D15 SOHC VTEC engine. The stock engine is a D15B2 SOHC DPFI (Duel Point Fuel Injection), so maybe the engine was swapped by the previous owner. Also it never came with rear disk brakes so maybe that also was swapped with Integra disc brakes which is common. The center console does have a AC button so that's stock.
Check the block again for the engine code. The engine identification code, as well as the motor’s serial number, is engraved onto every single Honda engine block. You can find the code on the exhaust side of the engine, to the left of the exhaust manifold, up near where the block meets the head. If it reads D15B1 or D15B2 then it's the stock engine. If it reads D15B then it's a JDM SOHC VTEC engine which means it was swapped.