I'm pretty sure that in all Honda B-series they have a common problem with the 3rd gear synchro which can make it grind gears when you shift..my friend just got a new gsr swap in his civic and his car grinds from 2nd to 3rd already. So it's no biggy :thumbup:
(To combat that nasty grinding you can try double-clutching for 2nd gear...my step-brother did that in his old Si cuz the gears were ****ty when he drove normally)