I'm not verifying any of this, it's just off the top of my head, so consider it blather until checked:
It's a 5-spd, right, not the CVT? The EK's S40 transmission is supposed to be stronger than the EG's S20 (steel vs aluminum shift forks, some larger bearings), so it might be a better match to your HX's 125 HP D16Y5 than anything that was mated with the tallest-geared S20 (92 HP D15Z1, 70 HP D15B8). About the only difference in gearing is that the S20 in the VX and CX had a 3.250 final drive, while the S40's in the HX is 3.722 - which is considerable. I don't know if the final drive gears from an S20 can be put in an S40 (I'm still looking into this), but if so then that would be an attractive option.
The non-CA HF transmission has a 2.95 FD and a slightly taller 5th gear too, but is cable actuated. I've seen converters for going the other way, but there might be kits to allow a cable tranny to hook up to a hydraulic clutch pedal.
One issue that I'd like to know more about when changing to a transmission with different gearings is how the ECU will behave. Purportedly, it is able to tell what gear you're in from the ratio between the tach and VSS signals, which will forever cease to match again if a differently geared transmission is put in.
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