I have a 99 civic si I just bought a few weeks ago. Last night at a red light my idle speed went up to 1500 rpms while just sitting there. After that, every time I let out the clutch in any gear it hesitates for a second then slams into gear. If that isn't bad enough when I let off the gas and press it again it also jerks back into gear. The shifter never pops out of gear. This all happened out of the blue. Normally the clutch felt awesome! There is no difference in pedal feel nor does the clutch slip at high rpms. I am at a loss at where to begin.
I can do minor repairs on my own cars but working 7 days a week gives me little time to do so. I also don't know of any trust worthy shops around my area close and I'm also afraid to drive it any further to risk transmission damage.

 

This sounds like an engine problem. When you say it is "out of gear" for a moment it is not, it is just that the engine is not making any power then it starts to fire normally again. Start by checking for ECU codes.

When you are out of gear the engine will rev up abnormally fast but the car doesn't go. It's not a "hesitation" that I think you are describing of you pushing the gas and nothing happens.

 

It does rev just fine when I push the gas as I am letting out the clutch. The jerking into gear is felt in the transmission not the engine sputtering.

 

When you get to where you are not pressing the clutch at all and floor the gas, is the engine racing, or is it at the expected rpm but the car not going?

 

The engine idles a little high without the clutch pressed in and in neutral. With it pressed to the floor idle is normal. The main problem is the higher the rpms when the clutch is released to go, the more it jerks into gear with a 1-2 second pause before engaging . It has kind of the feeling of when 1st learning to drive and you don't give it enough gas and let the clutch out too fast. Even if I were a new 5spd learner the trans shouldn't jerk when cruising after letting up on the gas slightly.

 

OK, in your first post you said you can be coasting down the road, not pressing the clutch or changing gears or anything, as you press the gas, for a second the car doesn't accelerate (and the engine doesn't rev), but then it jerks and starts to go. That is an engine problem.

If it doesn't really hesitate but you feel a jerk and hear a mechanical thud or banging noise the instant you change from foot off the gas coasting to stepping on the gas and accelerating, that could be a bad motor mount or CV joint.

 

I'm sorry for the confusion I've tried to explain this as best as I can since I've never had this happen before.
Imagine you are stopped. You push in the clutch, shift into 1st. Then you rev the engine and let out the clutch like you normally do to take off. As the clutch is to the point where it just starts to engage you feel the car start to move a little but after the clutch is all the way out there is a second long lag(engine revs normal) then it slams into gear as if I let out the clutch fast. It does this with each gear. Then cruising at 30mph in 4th gear I let up on the gas slightly to slow down just a bit then hit the gas again and then I feel a sharp jerk and thud from the transmission.

 

Sound like you did some burn out when you got the car, sorta abuse the clutch a little??

Your clutch is chattering, will need to resurface/change flywheel, then might as well replace the clutch set.

 

How do your two torque mounts look? bottom side of each frame rail...

You'd be surprised how much bucking you'll get if these are cracked.

 

It could be broken springs on the clutch disc, but absolutely rule out the motor mounts and CV joints before taking apart.