Clutch and transmission problem

I've been doing auto repair and work since I was 15 and got my first car. I've worked on Chevy's, Fords. Dodges, you name it, I've done it at one time or other. So mechanic work is nothing new here. OK, PROBLEM my jeep's a 2010 6-speed standard shift. all part are factory. I decided to install a complete , clutch package, clutch plate, disc, throw out bearing, pilot bearing, slave cylinder, and new trans mount. all came out easy enough, every thing went in easy enough. The real problem, after working, and working some more, finally got the slave valve to go in enough to release the clutch. so now have to push pedal to the floor to do so, when let off it makes up close to the floor. more than the old one. With the pedal up and trans in neutral the through out bearing is slightly touching the clutch finger, but you can take your finger and thumb and rotate the bearing with little effort. seams like the slave should move in a little more, when the pedal is pushed down, I don't know. Next problem, I had taken the trans shift tower off, trans was in neutral , nothing had been moved. now I have problem shifting into gear, especially reverse. I've never ever had a problem in my life like this crap. I love my jeep, but I thing engineering, should put a little more time in their work. What's the cure for this problems. HELP appreciated checked some more , with the engine dead, transmission shifts. as always, problem start when engine is started up then its hard to get in gear