I just got myself a 99 Civic last week for $3488. The body/interior is in great shape and the engine has 170XXX KM. Obviously at the price I'm going to expect problems.
The main problem I noticed was this sound the car would make when in N, almost a clanking sound. When the clutch was pressed in this sound would go away.

At first we where told it was a throw bearing. And they would have to remove the tranny to get at it. Today I got a call saying it was actually something to do with the tranny and he would be able to get me a used one for $700.

I'm also getting the clutch, timing belt, water pump, belts, oil changed and the total came to $2400.

He said it was a transmission bearing problem. Does this seem right?

 

ouch! Thats pricey, usually you can just replace bearings unless theres more than that wrong with it, $700 for a used tranny sounds kinda steep even for a junkyard price, if you look around at all you can get D series trannys for next to nothing, i have a friend that got an EX tranny for $150, and that was with new bearings in it too. DX trannys i've seen range from around $50 to $150, EXs are usually more $150 - $200, a wrecking yard will charge more though, my point is if you look around and buy the parts, even if your not putting them in you can some some serious cash. Water pump is something like $50 i believe, timing belt should be around $40 clutch should be in the $200 - $300 range oil change is like $30 the thing is, everything save for the oil change is labour intensive, so your gonna get raped there., even at that it seems a little high or i'm not charging nearly enough money.