There should be no issues provided that the transmission is truly from a 1988 HF. 1989-1991 transmissions have a different number of teeth on the input shaft spline (20 vs 21), and will not work unless the clutch and/or flywheel is changed to be compatible. Just keep in mind that sometimes, people DO swap different transmissions into their cars, and make the modifications needed to do so. So there is a least SOME possibility that your transmission is from a 1989-1991.
One more thing. I seriously don't know how much this is going to help your MPG. Recently, my brother gave me a 1989 Civic DX. And I figured I would try the HF transmission thing to see if it improves my mileage. And guess what? It did NOTHING! ZILCH! NADA! Oh, and his car actually had an SI tranmission. I just don't think you can slap tall gears on any old engine and expect better mileage by default. Sometimes, the engine just doesn't run that efficiently at, say, 1000-2000RPM. This is probably especially the case with Honda motors, as they are generally not low RPM motors. For instance, my B18C5 powered CRX has 200HP, runs at around 4800RPM at an 80MPH cruise, yet still gets around 30-34MPG on the freeway. Most other engines wouldn't. If you REALLY want better mileage, I recommend a D15Z1 swap. Unlike the D16A6 you have, the D15Z1 actually WAS designed around a low RPM cruise. Of course, you could always try the HF transmission swap to see what it does for you. But don't be TOO disappointed if the only thing you notice is ALOT less get up and go.
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