probably didn't mess anything up i did the same thing when mine acted up. if there was no fluid in the bell housing and the master wasn't low then i doubt you have bad parts usually they leak when they fail but bleeding is near impossible on these trucks first you want to bleed the master and line best way is take it out of the truck and bench bleed it then deal with the slave after perfection clutch has a great youtube video on it but double there recommended 2 reservoir fuels to bleed slave. Also the fluid goes black idk why but mine is after only 5000 miles of having a 5speed in the truck but the bleeding process will entirely bleed the system of old fluid. But if you do decide to change the parts do the clutch and rear main seal while its out i didn't do my rear main and now regret it because shimming the trans back in caused it to leak so i have to drop it again anyway.
New DD-2009 Ford Mustang GT/CS candy apple red.
(sold)2003 XLT Tan 3.0L V6 5-speed, Lots of mods.