I have a 99 accord manual tranny. I ran into a problem, the through bolt the connects the strut fork to the lower control arm will not come out on the driver side.

The same throughbolt on the Passenger side came out but not on the driver side. The nut came off on the through bolt, but i tried hammering, and torqueing the through bolt off on the opposite end of the throughbolt and no luck. any stories wit experience on this?

Thought you were talking about the hub/knuckle where it meets the LCA, but I re-read your post and am now not sure.
Get some heat to it if need be.

sorry man it was late at night, I am assuming a torch right?
**BUMP for correction**

When I changed my struts I had to put a jack in with a wooden block from the rotor up to the inner top fenderwall to line it up when I was trying to get the bolt back in, but I didn't have a real problem getting the bolt out. My problems were mostly with the passenger side but I'm sure either side could give issues. Just play with it or have a friend pull slightly up or down while you try to hammer it out. It'll come out, it's just probably caught. There is no need to try to torch it at all.

most of the time they rust into the bushing and not come out very easy. spray it down with some pb blaster and let it soak for a while and retry.

tried that but i belive the through bolt is packed with greese therefore the pb blaster isnt working.