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A '97 with only 40k ? Wow ! Sounds like a transmission issue. I would begin with changing the transmission fluid and filter. If that didn't work, I'd take it to a transmission shop because there isn't much you can do on your own with a transmission due to their inherent complexity.
The emission light came on because when you had the gas cap open the "EVAP system ran its test and thought it detected a leak in the system.The light will clear itself after it doesn't se the same problem after a set amount of drive cycles. make sure you keep your fuel cap on tight to prevent this in the future.
The 96-98 Civic EX came with an OBD2A D16Y8 engine. That is the only engine that will go in as a direct replacement with your current engine ECU. It's an SOHC VTEC engine that has two extra connections not found on the other 96-98 Civic engines - a VTEC solenoid and a special oil sensor used to determine if VTEC engagement is possible. If you swap in an older Civic engine (92-95 generation) you'll have to convert the car to OBD1 (requires a special adapter hardness) and run the ECU that goes with whatever engine you use. This will break functionality of your OBD2 diagnostics port, and depending on which state you live in will cause you to fail emissions checks. If you install a D16Y8 engine from a 99-00 Civic EX, you will have to swap the intake and exhaust manifolds from your old engine to the new engine, and you will be able to continue to run your existing OBD2A wiring and ECU. The 99-00 Civic EX engines have additional sensors, since those engines are OBD2B. The easiest fix would be to find a SOHC VTEC D16Y8 from a 96-98 Civic EX, as it would be a direct plug and play replacement.
Check the connections of the bulb sockets and the contacts on the bulbs themselves. Sometimes a small amount of corrosion or oxidation can increase the resistance in the circuit enough to cause the flasher to cycle erratically. When the fast flashing occurs, check both your front and rear bulbs. Is one dimmer than the other? If so, start by checking that one first.
While unlikely...does your Honda have any sort of towing capability? If so, corrosion or a short in your trailer light connection can also wreak havoc on a flasher. If your car has a tow hitch, you may want to remove the trailer wiring adapter from the car's factory wiring and see if the problem disappears. If so, either remove or replace the defective controller.
Check your wires, plugs and coils. I think it is an ignition problem myself. Something is breaking down under a load. My guess would be a bad coil or wire, the hard starting could be a symtem of this also, As I first read your description I was thinking maybe a leaking fuel injector or faulty fuel injector, but I believe it is in the ignition system. I hope this Helps! Merry Christmas!