the codes according to the shop are water in the fuel, crankshaft sensor, and another one fuel related i can't remember the exact terminology. I will double check to see what the scanner acutually coded it as

Please be sure to post back here. How often is the water drained and how often are fuel filters changed? What filters are used?

I drain it once a week it only takes a minute. I have only had the truck a month after an engine swap and the filters weren't completely shot but I decided to replace them anyway i used the purolator filters.

I would stick with international or motorcraft only for fuel filters. A lot of those aftermarket one's don't even have the water separator membrane built in... and this makes a lot of sense if you have water in fuel codes...

Could the filters keep it from starting or is that just for the water in fuel code?

the water in the fuel could keep it from starting..

but you say you regularly drain it, i personally dont think its the issue. unless your filters are totally plugged...

have you ever at any time noticed what looked like metal flakes in your fuel filters?

your seeing smoke, your FICM is probably working, this probably isnt fuel related.

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while your mechanic has it on a scanner, can you have him check what the hpop is putting out for pressure? i understand this is only as good as what the icp sensor see's but itll help.

I would still like to know exactly which codes you had. Can you get that info? That will help us tremendously.