Hey, nice job with getting the 'proper' tranny. Tip menbers might hate me for that. Anyway, I think I know exactly your situation personally. So that resistance.. If it is when you are letting out the clutch, it is the engine braking. Like it is slowly you down by raising the engine rpm. Also known as downshifting (which you already know). Anyway, I've always considered the 01A 5 speed manual to have a very awkward spot in the range.. Right at around 10-15 mph. If you shift into second, you lug the motor = no good. You shift to first, you throw yourself around = not comfy and makes you look bad to some. SO! If you are closer to 10mph, slowly press the gas when the clutch starts to grab, and that way you won't abruptly slow down with the engine braking. If you are closer to 15 - 20 ish, do the same, with second. Don't give it too much gas. It' may take some practice, but you just basically use the gas pedal to smooth out the clutch in awkward places like these. Hopefully that helps a little bit. I'll be around for awhile if that wasn't what you meant :p
Edit: The shuttering that you described, likely linked with the whole car vibrating, is just lugging the motor. Basically your engine is trying to keep up with a tranny thats RPMs are very low, and it (the engine) isn't designed to run that low. So if you were to keep slowing down without going to first or neutral, or shift into third, or higher at that point, you would stall your engine, and have to fire it back up. Lugging isn't going to kill your engine, but try not to make a habit of it.. As the internal vibration at those low rpms is not going to do an engine any good.
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