I came across this one thief, that kept stalking me when I was solo roaming in wvw
but I had some nice, spontaneous fights with him. Sure I made few mistakes but overall this fight turned out to be somewhat decent duel. Have a look. http://www.youtube.com/watch?v=_b8pph6cwZ0
Guardian vs Thief
A medi guard should be able to take a thief of any spec out extremely quickly
Use this sort of rotation next time, you will do a lot more effective DPS.
Focus 5 > Focus 4 > Scepter 3 > Scepter 2 > Weapon Swap > GS 5 + JI + Smite > GS 4 OR GS 5 Pull > GS2.
If the scepter 3 lands, and he has no withdraw/shadowstep to get away, teef is dead.
But yeah, more practice with your JI combos and you will improve quickly. JI is the most important thing ever in guard build because it lets you land mega bursts.