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If you look inside those emergency/exit lights that come on when then power goes out, all the batteries fit in there laying on their side.

How about flipping it over and pressing it out from the other side?

You do notice the extra power in the mid range (4000-6000) when the timing advances too.

I was just out on my 400, in the cool weather, with the HPI and it runs so smooth. It never skips a beat. With the  LED headlight and taillights I never have to charge the battery either. 

A little more run time and I bet it will look more like this with the 1-2mm ring and brown showing up.

Huge weight difference. I've had mine for many years. I never lapped it to the crankshaft but use a hardened thick washer on the mount bolt and have not had a problem. I use a timing light and precisely set the timing, install some iridium spark plugs don't even think about the ignition system for the next 12 months.

When you guys say 1 pin do you mean 1 pin goes all the way through the shaft to the other side so both sides engage the gear wheel? The 400 pumps I've tinkered with, that have the primer wheel, it's a blind hole on each side where the spring bottoms out and then the pin goes in.

Reference for those that have never seen how tiny. 

With the Dave F mod it should have a needle jet like the one on the right, has that been done? If the bogging is acting like you shut the key off, then try making it richer.

The metal tab you bend to adjust should touch and load the piece of spring steel. That is closing the electrical contact on the other of the coil and giving the alternator field coil (the rotor) voltage and magnetism. That is causing the stator coils to produce voltage (when running). Battery voltage is running through the coil in the voltage regulator and when it gets high enough the magnetism pulls that plate, above the coil, down. That plate is fighting against the pressure you have put on it with the bendable tab pushing on the spring steel. When the voltage is too high, coil pull plate down, contacts break open on the other side and stop supplying voltage to the field coil (rotor), reducing the output of the alternator. That is happening very fast, keeping the rotor voltage exactly right so it is charging at the exact right voltage. The more you bend the tab up, the harder it is for the coil magnetism to pull the plate down, thus the rotor is staying on too much and alternator output voltage is going to be higher. The less pressure the spring steel has, by bending the adjuster tab down, the less the output voltage will be because it is easier for the coil to break the contacts.

Cover plate. Look can look up oem parts at several web sites.   
https://www.yamahapartsmonster.com/oemparts/a/yam/50041822f8700209bc784eb3/transmission

You could rotate the crank, with the cylinder off, so the rod is at BDC and look to see if the rod is evenly spaced between the crank flywheels and not leaning towards one side.

I had a job working at a machine shop, many years ago, doing valve jobs. Some of the heads would come in that were run for months, skipping away, after burning a valve and they would have a big pie slice shape gone out of them.

12-18 foot pounds torque and blue locktite is good. Then check the timing and adjust as needed.

Something tells me sooner or later Amazon is going to look at the tracking and ask if you got it, but there is no signature, so..