ja240sx

just did a auto to 5 speed swap on my 90 240sx. i used a 1995 tranny with a 90 manual drive shaft, we started the car, with the back and the front jacked up. we put it in gear to see if the wheels turned and they did, but in a few seconds we noticed smoke. at the end of the drive shaft where it goes into the tranny, few of the bolt on the driveshaft are rubbing on the tranny tail, and the black plastic part was burning. my questions are
What should i double check?
is there something wrong with the driveshaft/tranny combo?
plz any input would be nice, this is the only thing keeping me from driving my car

ja240sx

BTW It's a ka24E and i used a 95 Ka24de tranny with a ka24E manual shaft from a 1990 also. only a few of the bolts rub. maybe 2 or 3 of them. should i use half of the s14 drive shaft and bolt it to the lower s13 one?