Why won't my 2000 accord go into 1st gear when the engine is running?

Start with the basics. Is the slave cylinder properly blead? I bet it's something simple like that.

what it does when it's not running is not connected to what it does when it is running- any clutch/tranny is like that- when doing a major repair like that, it's best to do one thing at a time so you can see the effects of your work- in this case, you should have waited to mess with the hydraulics until you could tell if you put all the mechanics back correctly- oh well, now you have to see if it is the hydraulic system- hopefully, it is, because you do not want to take it all apart again- I would replace the clutch master, too, the whole thing should be done, then make sure they have no air in the system- while it is up in the air, have someone pump the clutch pedal, and watch to see if you are getting any action out of it-