Ok i just got done swapping the nv5600 from a early to late model i installed a new clutch and fly wheel from autozone (dont have funds for a south bend) but now the padel is soft till right before the floor then it releases but dont seem to release fully cluth hydros were no opend but hang under truck for a month waiting on new trans could this hace messes them up

If the hydros were not opened they should have remained ok. Just to test, try pumping the clutch and see if it brings the pedal up. When my master cylinder went that is how my clutch acted until I got all the air out it. This would eliminate that as a problem. What clutch did you put in?

If the hydros were not opened they should have remained ok. Just to test, try pumping the clutch and see if it brings the pedal up. When my master cylinder went that is how my clutch acted until I got all the air out of it. This would eliminate that as a problem. What clutch did you put in? i understand limited finances.

Might have to do the bleed procedure to fix it.

http://articles.mopar1973man.com/2nd-generation-24v-dodge-cummins/28-transmission-systems/54-hydraulic-clutch-master-and-slave-replacement

Ill try bleeding it. Its a dura last clutch was there a difference in slaves fot the 12in clutch and the 13

No. I still got stock hydraulics in my truck with a 13" clutch.

Ok well i will try bleeding it if that changes anything ill get a new slave master system if not i guess im pulling the trans back out which sucks balls big time

If you pump the clutch and it does not help or bleed the system you have and it does not help, dont buy a new master/slave set up because it wont help either. If you did not see any fluid loss from the hydros, that is most likely not the problem. I looked on Rock auto at slave cylinders for the 00 and the 02. While there were several different shown between the the two, there were several of the same also. 

I havent really tried that yet but i noticed it seems to be some what better in the morning after setting over night

Thanks for the advise after some priming and use it is back to normal 

good to hear.