Unable to get first gear.

sounds like the charging system is not charging when the battery is low the starter will not disengage properly disconnect battery and charge it while battery is out with bike in a high gear 4th 5th push bike back and forth this should unengage starter once your battery is charged and back in bike if the starter engages and dis engages properly then you will need to test your stator output with a multi meter look on you tube for video to test stator good luck

This is a strange fault with a new bike. What happened when you pulled in the clutch lever? The clutch is unlikely to be stuck after that period because its internal and runs in oil anyway. You need to better explain what you were doing at the time. Was it running and you couldn't get it into gear? Yamaha's are great bikes and at 6 miles I'm a bit baffled.

its an alternator not magneto, there should be 3 wires white or yellow, going to the reg\rectifier, multi meter across any pair(unplugged) should show 50-80 volts at 2000rpm non of these should short to earth, multi meter across battery should show up to 14v at 2-3000rpm.with everything plugged back in
if alternator checks out, and no voltage more than 12 at battery , replace regulator,,

all assuming the battery wasn't fried when it ran out of acid

my guess is new stator\alternator required

Have a bike service center checkout the gearcase. It sounds like it's shot! Especially with the age of it.

It's "Shimano". SRAM and Shimano are the main players in the bicycle component industry. Each has boutique parts and throw-away parts. Guess which end your your bike is on.

Visit their websites to look around at the offerings. Just the parts on a high end bike (no frame or wheels) can set you back $2000.

The problem needs some better definition and a trip back to the seller for evaluation. OR bite the bullet and get a better Bike Shop bike that will come with a relationship to the guys at the bike shop, who are always ready and willing to advise you.

More than likely the shifter pawl has broken. Breaking in 5th gear is kind of unusual however, they usually break between first and second.

You'll have to remove the outer primary cover to look at the shifter pawl. It's partially covered by the clutch assembly.

sound like you have a leak from the head gasket and its drawing air if you have no knowlege of motor maintance stick it into the shop

The bike is 6 months old, or the chain/sprockets? Either way, sounds like you need a clutch.

check the battery or possibly the bike was in gear with the kickstand down

Do check if not drain and refill the gear box, but check with your dealer that it will not affect your warranty. a little self help may prevent time consuming and inconvenient repairs at this stage, but remember gears are clunky and come in for a lot of abuse, reliable as they are.