You are wrong on a few things.Shifting at the lowest possible rpm's suggests what some call "early shifting". If you switch from 1st up to 2nd too early then you put unnecessary strain on many of the parts working together to move the car. Shifting at a lower, rather than higher rpm will save fuel, no doubt.The best time to shift from any gear upwards, with the exception of 1st gear, is when you feel that the engine is pulling with less strain. With my Civic that is around 2500 to 3000 rpm. If I hold the shift longer and achieve greater rpm the car will continue to move forward at a greater rate until the next gear is selected. As you drive around and choose different shift points you'll see what I mean. Also, it is better to shift a bit later ( slightly higher rpm) than too early as rpms will not do any damage to that engine.3rd gear issues are yours and not the car's gearbox.Consider how the shifter moves and the distance it will travel. It is common, if we slow it down for a second, to move it upwards from 2nd, a bit to the right, then upwards into third when performing the 2-3 shift. Try this instead. As you clutch in to disengage engine from gearbox simply push the shifter with a light touch upwards towards where it needs to go to grab 3rd gear. The shifter will move upward from 2nd into 3rd on a "path" and you don't need to be deliberate with the movements. The same technique can be used for 4th to 5th movements.I'm on my 4th Honda Civic and they are by far the smoothest, best feeling manual gearbox equipped cars on the market and I think you may just need some practice.