2007 is torqued properly from the factory...

Don't mean to offend you, but make sure you depress the clutch completely

Try pushing the clutch down twice before putting it in gear.

Once in a while my car does the same, you can feel the resistance is greater when it's about to do that, so I ease it in... ahem...

I would say change out the tranny fluid, but with 800 miles I wouldn't

Have you been flogging the car and NOT following the break in procedure?

You might require a adjustment, I believe it's the clutch rod. But I think you should leave that to the very end (I would get Honda to look at it first)

 

My diff was "thumping" because it broke a tooth off the pinion gear. Minimal metal particles in the fluid when I checked it.

The tooth broke cleanly off and was sitting in the diff.

 

I properly broke in the car, and I bought the car with 41 miles. For the first 559 miles, I careful drove my car, but I don't know how it was previously treated.. This is my third manual transmission car, and it only does it once in a while..

 

Whats the diff?