You are right here, it is a matter of breaking the long developed habit.
Most of us have this handicap. I had used a two wheeler from 1990 to 2007, so about 18 years experience of riding two wheels was behind me, when I started using a car - Yes, my total experience of using a car is about 3.5 years, 40k km. However, I have learnt a lot from CW. You can too.
Not using clutch for anything other than changing gears or starting from standstill is a very good practice. I too go the ingrained two-wheeler way sometimes when I am not conscious about it, but as far as possible I try to use the brakes without using clutch.
One thing you can start doing is, choosing your gears such that the running RPM is maintained between 1500 and 2000. I have seen best mileage being returned by the car when you touch the throttle just lightly and maintain 1500 RPM. However, with these conditions (usually in top gear) the speed achieved is only 50 KMPH, so people choose to go upto 2000, with some penalty in FE (Fuel efficiency/Mileage).
If the RPM starts to go below 1500, choose the lower gear, and lay off the clutch. If you keep doing this all the way to first gear, (below which you can't go anyways) you can even crawl through traffic in first gear without using clutch. But sometimes, you do need to use it.
Maintaining the 1500-2000 rpm helps you in good effective AC as well, because AC compressor runs on engine speed and not vehicle speed.
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