On my first ride after the engine rebuild, I drove it to a neighbor  hood incase I broke down I wouldn’t be stuck on a main road. The thing was running mint and about 7 miles in I got 2 backfires as loud as a gun shot, then it wouldn’t stay running. People were worried coming out of there homes lol pretty embarrassing but does anyone know what could have caused this? 

Exhaust or intake backfire?

Exhaust backfire, I pulled the end cap off the exhaust and there doesn’t seem to be a baffle or spark aresster in there

First thing I'd check is timing. 

Also spark plug gap and condition.  Sometimes you get an exhaust backfire when plug starts to fail.  Make sure gap is 0.020" to 0.024"...  not the 0.032" it probably came in the box with. 

When I installed the magneto/flywheel I set the timing gap to .0013 at TDC I’ll check to see if it moved. And it’s a brand new spark plug set at .028 I’ll close up the gap a little. I appreciate the feedback

Not sure if you misspoke but that's not the correct timing.

Points should just open at 1.8mm BTDC. 

You don't "gap" the points.

I’m not sure if this link in going to work but this is what I used as a guide as far as the timing goes @27:05 in the video

I was going to say that guy doesn't know what he's talking about....  Then I went back a bit further and he appears to show how to set the timing back around minute 20.  That's what you need to follow.

At 27:05 he shows CHECKING the point gap at maximum opening (not TDC)

On your engine you NEVER "adjust" the point gap. You set the timing and CHECK the point gap.  If you were to adjust the point gap after setting timing correctly, you'd screw up the timing. 

Experts like DEET might even say don't bother to check the point gap at all.  I don't disagree. 

And RT325 will probably jump in and say timing can be made "close enough" by setting points gap to some number.  (I don't like this method because you can hole a piston if you use too big a maximum gap...  but it can get you home until you can do it right)

But you're having a problem and didn't do either...  (TDC and "max gap" are not the same thing).

Your bike, your choice. 

P.S.  I don't have the patience to watch the whole thing.  So not saying he didn't make misleading statements or anything.  Yamaha factory manual method is 1. Set Timing.  2. Check maximum point gap and make sure it is within specified range.  (usually 0.012" to 0.016" or something like that.)

I have never checked the points gap I was taught to set the timing when I worked at Butler Yamaha