1st and 2nd gear keep jumping out of gear - 1999 Yamaha V Star 1100 Custom

You may want to make sure the clutch cable is properly adjusted. At the clutch lever on the handlebars, pull back the rubber cover over the end of the cable where it goes into the lever. You'll find a round lock wheel that you tighten to prevent the clutch cable adjustment from moving. Loosen that wheel then you can turn the clutch cable adjustment in or out to adjust the clutch engagement and take up. For those bikes, you want to adjust it so that there is a small amount of slack in the clutch lever. Look at the "crack" where the lever pivots when you pull on it. Adjust the clutch cable by turning that adjustment in or out until you have just barely enough opening to slip a nickel edge into the very outside of that "crack" when you apply very, very light pressure to the clutch lever (just enough pressure to take the slack out of the lever). Tighten the lock wheel back into place and try it now. Also, make sure you are using a good, FIRM foot pressure to engage each gear. If you don't engage firmly enough or the adjustment is out, then it will pop out of gear. You notice it more on the lower gears because the lower gears allow the engine to send more torque thru the clutch, thereby providing more force to make it pop out of gear.

If this doesn't help, then take it to a shop to see if it's simple worn clutch disks (easy to replace on this bike) or if the gears have worn teeth in the transmission.