i have a miss

[novarider]

hi im new to this forum i have a 95 240sx and it is missing, sometimes but not all the time, and the check engine light is on so i went to the shop and they told me it was a bad egr valve and a knock sensor. but they told me to do a tuneup and see if that fixes it. i also have that rattle noise from the timing chain so i was wondering if it could be that the chain is so loose that it is the reason for the miss? the miss started after i replaced the alternator and when i replaced the altenator i forgot to plug in the wire and the battery died and i had to replace it then got the wire hooked up and then was driving and the miss started is the altenator just a quaincadince or what i really need some help thanks for any replys