I also own the santro Plus 2001. But its GX with EFI engine.
I had the same problem, which was rectified by the GarageMaster behind the Urdu University Islamabad.
He asked me to change the plug wire ( which I know you have already change), but when I replaced with the orignal one from Hyundai which was about of Rs1800, that solved my problem.
does it misfire even on petrol?
try reducing the spark plug gap. or check you plug wires resistances to check if it of any good.