Ok so I think I got this figured out. I have plenty of threads if I get it true flat again so that's not a problem and it's less than 3\16 of a taper so the impeller or shaft nut won't hit the bowl so I'm going to take it to machine shop Monday and when they get it flat ill see if the bowl rubs on anything and if it does  I'll toss is and buy a new bowl if it doesn't hit anythig and bolts up flat I'll run it right.

Or was this some backyard build

You say you have history with this pump?  First, the questions before a possible solution.

Why did you take apart?

How did it look when you inspected it?  Were there signs of rubbing?

Were the bowl bushings just needing freshening up from normal wear or were the old ones through because the shaft was binding from bowl misalignment?

Was the pump making noise?

Are the impeller and wear ring showing unusual or uneven wear?  Any burn marks from repeated or continuous contact?

Did the bowl gasket leak or fail?

If you can say;  1.) You didn't have any serious issues with the pump before.  2.) There is no rubbing or tight spots with all eight bowl bolts torqued.  3.) You didn't have any bowl gasket issues before.  I might suggest running it as is.

Be honest, failure could destroy the entire pump at the most inopportune time.

You might be able to get away with running it as is.

For the record, I would scrap it regardless.

The housing had a Crack from the bottom right bolt hole to top and the boat was taking on more water than normal. That's why it came out. After seeing where the crack was and now knowing that the bowl wasn't flush the bolts being tightened on the bowl cracked the housing. It ran fine just started leaking water from one to many hard runs I guess.

So the bowl is somehow matched with the housing so the pump doesn't kill itself or bushings by being not straight. If  I buy a bowl how would I know it's going to the same angle as the suction and shaft or am I over thinking the whole thing. 

Oh, now I recall

I would put The feelers out for another bowl.  At this point, I am not prepared to go in to depth on the topic of inspecting a used bowl.

If you go the machine shop route, make sure they have the capability to make that surface perpendicular to the bushing bore centerline.  I would write that on the part before you drop it off.

Right just sayin