Didnt have much time to mess with the bike today but i was able to pop a bulb out of a spare gauge 6v3w and swap it out with the indicator light i currently had in it. Made it blink faster. Took it for a spin down to the neighbors, bike lost spark, i swapped the indicator bulb i previously had in back and now that one too seems to blink faster with the bike shut off when before it was a normal pace. I gotta get spark back and clean out that check valve on the oil pump mark T pointed out before i can focus all my efforts on the electrical.

I'd try a different flasher. Good ones are not that "sensitive" to a small change in load.

MarkT im going to PM you the flasher i purchased. Having some trouble posting the link here.

Ebay link to flasher

Since you've been an active member here for quite a while, I feel like borrowing a line from...  I think it was an 1970's advice column in Dirt Bike magazine written under the pseudonym "Mr. Know it All"... 

"You should have known". 

Unfortunately, I don't have the comedic talents of Rick Sieman (aka Super Hunky) or some of the other writers of that era.  I wish I did. 

If what you bought matches the ebay photo, it's a modern three-wire flasher with terminal X, L, and P.  It might work if you only use two of the three wires. (If it hasn't burned up)

X = Battery - Solid brown wire on your Yamaha
L = Load -  Brown/White wire on your Yamaha
P = Pilot - NOT USED ON YOUR STOCK YAMAHA, tape it up, DO NOT CONNECT TO BLACK GROUND WIRE that went to original flasher!

(My guess is you have crappy ground connection that makes a better connection when revved up which is why it starts flashing super fast? Miracle it flashes at all if it's what is show in the picture)

Anyway, if you didn't read any of the hundreds of posts here talking about modern three wire flashers and how you actually need a two wire flasher, the wiring diagram the ebay seller provided shows a correct original (very obsolete!) type flasher with different terminal markings for two of three wires than the one being sold.  (Red flag? Yes.)

B (equivalent to X on a modern flasher) clearly goes to the Battery power in the seller's diagram. (New flasher doesn't have a B terminal)
L (same as L on modern flasher) clearly goes to Flashers (or "load") in the seller's diagram
E (Almost impossible to find these days) goes to "Earth" or ground.  (New flasher doesn't have an E terminal)

So the flasher shown in the ebay pictures has different terminal markings than the one in the ebay seller-supplied diagram...  not sure how you decided to wire it?

(Or of course there is a small chance seller sent you something different than shown in the ebay ad pictures and your new flasher does have B, L, and E terminals?)

Anyway, try connecting the X to brown and the L to brown/white and leave the P disconnected and taped up so it can't short to anything.  Do not connect the black wire to the new flasher. 

Hopefully this fixes it.  Fingers crossed!

I appreciate all the info! during my search on here i did see 1 post about using a 2 prong flasher but i didnt dive much into that because i was thinking 3 wires=3 prongs. I currently have it hooked up as X solid brown, L brown/white and P black. Ill disconnect that black wire and tape it off like you said. Hopefully that does the trick because im sick of electrical. Definitely my weak point on these bikes and this is my 1st time doing all the lightning.
Before i worry about the electrical i gotta get spark back. Most likely points but ill post back once i get things figured out.

Just to be clear, the P terminal on the flasher needs to insulated, not the black wire.

If you had a stock flasher and it didn't work, it's possible it's because the black wire to the flasher doesn't seem to be a good ground... if it was, with it connected to the "P" you would have likely been blowing fuses as it would be direct short to ground. (You are using the stock fuse or other 10 amp (max) fuse right after the battery correct?)

You said you don't have time to check the electrical. I strongly suggest you do not turn the flashers on until you correct the flasher issue as you could have an electrical fire or damage something like the key or handlebar switch... just because it didn't happen yet doesn't mean it couldn't.

I'm also mentioning this because you said you lost spark... please be sure your grounds are good. Especially if frame is powdercoated or freshly painted. Engine needs to ground to frame solidly through the mounts. Ignition coil and all ground wires also need a solid connection to frame or you will have no end to oddball electrical issues.

Yup i will get that P prong insulated.
When i first hooked all this up and was testing the lights with the bike off the blinkers did light up but never flashed. Plus i could hear the original flasher relay make a funny noise. I took it off and did tear it apart and while doing so the metal piece that the black wire hooks to broke in half. I believe that metal piece touches the inside of the "shell" which grounds it. I was planning to try and fix it after i was done with the bike.

My fuse is a 6A32V. I had to buy a fuse holder and splice a wire or 2 because someone had cut it but luckily thats all that was cut on the harness.
As for spark my points were way too close together and ive got her sparking again. Im going to pop the head off to have a look in the cylinder before trying to fire her up again. First time doing the oil injection pump and i have trust issues. I did sand some grounding spots a few months ago so the motor could ground to the frame and the handle bars to the frame.

Well i got spark back and shes running great now so its back to my fast flasher issue. I unplugged the P/black wire and insulated the prong on the flasher relay like you said Mark and still no luck. Still flashing fast when engine RPM goes up. Im wondering if maybe i should run the black wire i unplugged to a ground on the frame maybe? Perhaps i should try popping the 6v18w bulbs i have instead of using these 6v8w bulbs?

If your black wire is truly a ground, you would have a direct short through the flasher. Normally when someone connects P to black (ground) the fuse blows instantly.

In your case you might have fried the flasher unit? Who knows.

I don't think i fried the unit other wise it wouldn't work at all you would think. Ill swap those bulbs out for the higher wattage ones and see what it does real quick. If no luck ill go back to the original and try fixing it. In the mean time i still gotta clean that check valve in the oil pump and get this clutch adjusted. I need longer adjusters up on the perch, their so short!