i had the same problem, 2000 gts though. shifting into 2nd i would always get this hard bite awful grinding. i ended up avoiding that gear totally. upshifting 1-3 and pulling out of turns in third.
my specific problem was the clutch not disengaging. the shop pulled the clutch pedal out further so it would disengage sooner, but still you had to push literally your foot into the floor to shift.
double clutching smoothed out the shifting but was horrible to have to do with a car with only like 28,000 miles at the time.
had to replace the clutch and transmission. other related problems occurred later but now everything is fine.
guess your vehicle is not under warranty, so hopefully they can just replace the syncros not the entire transmission. the dealership was saying that the transmission was like $4 grand or so. luckily for me a toyota rep was there and my vehicle snuck in three months prior to the original warranty was up...
good luck, a large chunk of my cost was shouldered by toyota and a dealership. but it was still a headache and still cost me quite a chunk of change. also, it severely impacted my aftermarket purse and set me back for a few months...