Good. This helps move forward. Going off 99 there was no b20b in a civic. That engine, if I remember right came out of the CRV so the engine isn't native to the vehicle. Also, LS transmissions came in both hydraulic and cable, this could be the key point being that this thread is transmission related.
What do you mean by rust. Where is the rust? Have you inspected the transmission and the cables/lines for binding? What have you done so far to pinpoint or troubleshoot the problem? How is the fluid in the transmission? How many miles on the transmission? There are a lot of factors and questions here that aren't clear because the question is so vague.
Just shotgunning based off your first post, you have internal transmission problems if it isn't going into gears. Weather that be low on fluid or messed up internals. But, it can also be as simple as a badly adjusted shifter cable if yours is a cable transmission. If you can't troubleshoot, I would recommend taking it to someone that can. A transmission shop, Honda, an independent shop that works on imports. Anyone that can diag this thing. There isn't much we can do over the net unfortunately.