The difference between the DX and HF isn't just the engine and transmission. The HF has lighter weight bumper supports, a front bumper lip, a partially blocked-off radiator air inlet, optional passenger side mirror, a lower capacity fuel tank, smaller axles, steering knuckles and front brakes, among other things. Honda really cut out whatever they could to make the HF lighter.
To get the HF engine in, you would need the complete engine with manifolds, the engine wiring harness and the HF ECU. You would need to adapt the DX's main wiring harness to run the HF's port fuel injection (the DX uses throttle body injection). This is commonly known as an MPFI swap - You should be able to find numerous how-tos on the web.
To convert to a manual transmission, you'll need the transmission (obviously), the shifter and shift linkage, the pedal cluster from inside the car, the clutch cable, all the mounts that bolt to the transmission, and the rubber mount that bolts to the rear crossmember. If you end up piecing things together rather than pulling the whole swap from a donor car, add a clutch and flywheel to that list. Your DX axles should work fine with the HF trans.
In my opinion if you have a bit of time and youa re willing to drive or fly you can definitely still find either a Civic VX or a CRX HF. It just takes frequent looking on a site like craigslist for instance. Using this site I have been able to find a totally original 1991 CRX HF with 150K on it for and recently a very nice original 1995 Civic VX. All this within about half year period. And these cars were both within a 3.5 hour range. If you'd be willing to drive further or fly your chances of finding one faster increase.
Since I can't believe that I just happen to be the luckiest guy on this planet I think these kind of deals are still to be had frequently enough (who knows for how much longer).
So my advice would be: wait till you find a good CRX HF if that is what you are wanting. Instead of spending money and the time in the garage, spend a bit of time every day online and find that minty HF
I have a 1989 crx hf. In my opinion all I would do is swap the tranny to a HF. The gearing alone will save you huge mpg. I am at 1600rpm @ 55mph or right around there. Sure the HF's were lighter but not that much lighter.
I have a 100k mile DX motor in my CRX HF with my old 220k mile HF transmission. I am 270 pounds, and I often carry close to 100lbs of stuff in the car and I am averaging 45mpg+ with normal driving no hypermilling. The swap added 50% more HP with the 16v engine. Excellent for climbing hills. The HF motors get tired at 150+k and many of them smoke. They struggle to get up hills. I know mine did. The DX is just a better motor. I am not sure how much the intake and manifold matter. The guy who did my swap used the HF intake and manifold I believe. Most likely because of the computer.
If I were you i would go for it if the body is nice then just swap in a HF tranny. They bolt right up. I bet you would avg close to 40 mpg or better. If you went further you could switch out the intake, manifold, computer, harness.
I wish my crx was in good shape looks wise. the body is a rust bucket but the underneath is rust free thanks to the undercoating that was applied when new.
I got it for 500 bucks and the motor cost me 100 bucks off craigslist which after selling the DX tranny only cost me 50. I had a guy swap motors for 350 bucks.
The best thing I like about my car is only costs 27 bucks to fill up at $3.45 a gallon and I get 350miles out of it. I had to drive a truck a couple weeks ago for a week and a half and that thing cost $80 bucks to fill up and only 360 miles.