Wow that's a real doozie. Maybe the trottle cable is too tight? If not, try replacing your throttle body; the sensor may be bad.
As for your tranny problem, I'm stumped on that one. I have yet to pull a honda tranny apart (tho I will do so soon), so I can't say for sure what's wrong. Here's another question: Before the car has warmed up, can you drive at higher speeds and still shift just fine? See how fast you can go and still shift before it's all warmed up (safely, of course). Let us know.