A D-series motor will bolt into an orignally equiped D-series car using that cars old mounts. As far as I know, the location the mounts and brackets actually attach to the engine hasn't changed, but the shape and design of the brackets has (B-series mounts bolt on differently and fit a '92-'00 civic chassis but don't fit the previous years and no OE mounts fit a B-series engine and the older chassis). There are however other complications to this swap. You will have to reuse your transmission. '88-'91 Civic's use a cable to operate the clutch while '92+ Civic's are hydrolock. The older tranny you have now will bolt to the new D16Y8 but unless it's an Si tranny, the gearing will be more oriented for gas milage than performance and it's going to hurt acceleration. Also, the D16Y8's computer will never be happy in a '88-'91 Civic. There are too many addition sensors and harnesses it needs to see to function properly that your car simply doesn't have. You can use your old ECU to control the engine, but the VTEC obviously won't work becuase the old ECU has no VTEC programming. There are probably other smaller issues but those are the big ones.

A simplier solution would be to use a '92-'95 D16Z6 SOHC VTEC (basically the same as a D16Y8 just out of a '92-'95 Civic EX/Si, but a closer match to the '88-'91's wiring). Somebody makes a conversion harness you can use to plug the D16Z6's P28 ECU into your car. There are quite a few additional wires that need to be run that don't exist in your cars wiring (especially if the '88-'91 isn't an Si and only has 2 fuel injectors in a direct port injection DPI setup) but it will work. Your still stuck with your old tranny and other issues but it will be a lot less frustrating than trying to make an OBD II ('96-'00) engine work. A 125hp SOHC VTEC isn't going to set any landspeed records but would be a good solid engine that's fun to drive.