First off, hello!  I hope this hasn’t been covered or is easy to find on here but here’s my problem.  
I just bought my first bike. It’s a 2006 s40. Had it jumped and it ran fine. I replaced the battery to get it to start but that didn’t work. Instead, the top fuse blows every time I plug in the rectifier. All the wires look ok. The indicators turn on but are solid, same with the hazards. I don’t get a neutral light either. Last detail is when I hit the starter the lights turn off and I get nothing. Easy fix?
Anything helps!  Thanks!!!

Just for giggles, I'd check the diodes of the regulator/rectifier.

Awesome places to start!  Thank you guys!!  
When I push the starter, lights off, but only while pressing.
I used ohms on all the leads on rectifier, all were reading even around 630.
I’m going to try these places tonight after work. Again, I REALLY appreciate the help!

Ps.
Climber manual is in the mail👍🏻

Art if your testing for ohms the bike should not be running , ohm meter set onRx10 , test the yellow leads coming from the alternator .outaside left to middle, outside right to middle ,and outside to outside .you should have very low resistance on all 3 reading if the continuity is good, and infinite resistance on any one of the reading if it's bad (I don't know how you came up with 630 ,it should more like 1 or 2 on the scale choosen.)
        If you want to check the output you need to change the meter to the 150 volt setting ,(be careful because output is AC  volts)do the 3 tests as above, but you'll have to have the motor running and raise the rpm to about 5000 to get a reading each time ,output should be at least 100 volts AC each time.
         A quick check of the regulator ,would be to check the voltage across your battery while bike is off, (a good fully charged battery should have a voltage a bit higher than 12v (12,3-12.7) then start the bike and check again the voltage reading should be higher (13.3 -13.7) is typical . 
         

I’m running!  Are you guys ready for the most ridiculous reason ever?  I hope someone else will see this and avoid the embarrassment of asking.

So, I decided to pull the new battery out and make sure it wasn’t crushing anything in there. Then I noticed the problem. Looking top down at the battery, I see +====-
Oreiley sold me the wrong battery!!  I was so excited to get it started that I didn’t realize when I put it in that the signes were switched!  I honestly can’t remember the last time that many expletives came out of me.

I'll bet you never connect a battery cable again without looking at the battery and make sure red is positive.