I think if you didn't sync them there's a good chance they're out of sync. A sync is good regular maintenance anyway. It probably can't hurt to check the plugs, Seafoam the motor, and sync the carbs. At the least, it should help reveal a problem if it doesn't cure it by itself.
What took the old motor out at 17,000 miles? And, how long did it sit before replacing the motor?
2013 V Star 1300 Deluxe
OEM Tall Sissy Bar
Memphis Shades Fork Deflectors
Bridgestone Exedra Max Belted Tires
Baron's RSTD 7308 bar