My 1100 Vstar back fires, and runs sluggish

Greg o day YOU DA MAN you also helped me with my 2001 vstar 1100 i was having same trouble with coils i tested the ohms ,voltage and spark every thing looked good but was still not running on front cylinder until i replaced the coils.

yes

sounds like a problem i had with my v star if u can charge it and it starts and runs for a bit then dies again check the rectifier which charges the bike

The timing chain most likely adjusts itself( I am not certain) however a loose chain will cause an engine rattle, but is not the cause of popping and dying.
try cleaning the fuel system, new spark plugs,new air cleaner

When Harley's spit through the carburetors they usually pull off the intake manifolds and reseal the them . New gaskets, o-rings, or even manifolds, whatever it takes to seal the intake. You may want to run some Yamaha Ring Free Fuel Additive ( Chevron Techron Fuel Additive) through the bike. A bad spark plug or spark plug cap could also be contributing to the pre-ignition that you are experiencing. If you can fix it yourself may be Yamaha will be kind enough to cover the parts cost if you are still under warranty and you are very polite in the letter you write.

did you get it checked for cylinder pressure? take out spark plugs, clean them out and observe for any oil or deposits