Picked Up an 07 PreRunner Last Week, Got Transmission Question

So last Thursday I drove out of a used lot with an '07 PreRunner with 108k on her...$8300 before taxes. Regular cab, manual everything (windows, locks, tranny). Bed has paint spilled all in it and tires have ~10k left in them...the only reasons I could comprehend the price. This is my first truck, first Toyota, and first standard transmission, so it's a lot to get used to at once.

When pulling the shifter back into 2nd (with clutch completely depressed), I hear a low-pitch thud almost every time. It's not something I can feel at all in my seat. Sounds kind of like rolling over a centerline reflector at 20 mph.

I have heard some reports of clunky-sounding standards in this year range. Just hoping this is not a symptom of a larger problem. Everything else about her runs like a swiss watch and it has been really a blast to drive for the past week. I can't believe I'm getting better fuel efficiency now than with my '00 Accord! Thanks for the help.

 

I have a 08 v6 6spd. Some times it bucks humidity is high, when or after rain. Sometimes clunks but never does it all the time. Truth is it bucks every time its rained. If was in the garage or out side 50% of the time after rain clutch chatter. I have 95k and my 1st clutch craped out at about 30k. Toyota fixed it no charge (long story) just my two. Have someone check it out.