Does not start after replacing intake valve cover and gaskets

So, took out intake valves and gaskets cleaned and replaced so once everything was back together, I started her up well at first it smoked a little and was running a little rough but then she evened out and sounded great ran for just a few minutes then shut off. So, after replacing the alternator and some fuses she ran great. I took her around town and all, so I go home then when I go to leave again nothing it's like all I hear is this click, click, click. My battery is good, I've had both the starter and alternator checked the last time and they were both good. I've traced all the wires to make sure they were all connected and still nothing. please help.