Slow cranking YFZ450 PLEASE HELP tried everything

Okay so here is the history from day 1 on the issue at hand... 2005 YFZ450 (big gun rev box, jetted carb, GYTR exhaust, no lid on air box)

- Few years back the stator and computer went bad simultaneously. The computer we determined went bad when the back wouldn't start up. (I believe this happened after hitting a large rock in the trail may have given it enough of a jolt). The stator went bad because the allen key bolts on the fly wheel sheared off hitting the stator and breaking apart the windings. The computer was replaced with a "Big Gun" rev box and the stator and allen keys were replaced with a OEM parts.

- September 2013, I had to install a tether style kill switch for a race. The following night (while upstate) I went to turn on my head lights and they did not work however my tail lights and brake lights worked fine. We tried to trouble shoot the problem but with limited tools and time I was forced to race with no lights. Quad ran great all weekend.

- October 2013, Traced the lighting issue back to the stator as the headlight are on there own circuit off the stator. This time the stator sheared off the engine cover, making the cover unusable as well.( this would mean the stator did not work for the whole race and weekend. So it ran strictly off the battery? and fired up fine every time, battery never felt weak) Under a tight deadline for the next trip I purchased a used case and stator off e-bay. (I know not to buy used electrical parts but the cover was too expensive new and the stator seamed to be good in clean condition).

- October 2013 (Day 1), I installed the cover and stator but did not have time to run the quad before loading it on the trailer.

- October 2013 (Day 2), Upstate I started the quad and still had no headlights, once again limited time and tools we decided to ride for the day with out the lights functioning. After riding for maybe 5 hours of trails, open roads, and jumps the quad died on me. This was after a good stretch of road in which the quad was almost at the top speed for maybe a minute or two. Thinking that the quad died due to the battery dieing as I hit the starter and got nothing we decided to swap battery with my Dads battery from his 2004 Raptor 660. The battery's were not the same size so we let my dads charge up mine for about 10min then stuck it back in mine. This gave it enough juice to start and get back to a road. From the road we towed it back to the trailer. We took the battery out of my quad and charged it on a trickle charger in the hotel room over night.

- October 2013 (Day 3), Took the newly charged battery and put it on the quad. the battery did not have the power to crank over the quad. We pop started it after pushing it around for a half hr. The quad ran like shit for about 2 min around the parking lot. While towing it back to the trailer i tried once more to pop start it and it just wanted to skid out the back tires. Frustrated we packed up and went home.

- November 2013, Tried to get the quad to run. Tried Pop starting it and the tires rolled freely but not enough to start. Pulled the spark plug and still cranked slowly. Tried jumping it off a 2012 F-150 and almost stalled the truck. (learned that this was a bad idea from Yamaha as it puts to much power to the quad). Bought a new OEM battery and still cranked over slowly. Gave the carb a shot of starter fluid and "BOOM" the motor locked up.

- November 2013, Pulled the motor out and determined the rod was seized to the crank. (thought this is why it was cranking so slowly) This was because of 1 or 2 things. Either the bad oiling system the 04-05 YFZ's are known for (which while I had it apart I did an 07 oil mod which added an oil nozzle to the top side of the crank and a higher volume oil pump) or when the stator blew apart a few pieces of coil were stuck to the oil pick up. I replaced the crank/rod and bearing with a stock stroke "Hot rods" crank, and new OEM piston rings. (no issues with the rebuild, everything went smooth and took our time, correct torque specs etc. followed the manual to the T) Left all the valves alone, never flipped the head over, simply unbolt and rebolt.

January 2014, Put the motor back in and fully reassembled. Went to start the quad and cranked over slowly. Pulled the spark plug and still kicked over slow. Disassembled enough to get the starter out. Disassembled and cleaned as per the owners manual. Brushes looked very worn but put it back on and gave it a go. Still had the same slow cranking issue. Bought a new aftermarket starter. Put that in and still cranking slow. Bypassed the starter solenoid and still cranked slow. Ran jumper cables (car size) from battery to starter and still cranks slow. Pulled the stator cover off and all the gears were put in the correct way.

All of this is without the spark plug in as well so I am not fighting any compression. Can spin the motor over by hand on the crank shaft and can spin the motor and trans freely by spinning the back tires. Starter spins freely when now on the motor. All gears seam to be mashing together nicely.

So the million dollar question is why is it cranking over so slow, so slow it cant fire up. (read a million threads and tried everything that I have read so far seams like I must be missing something but cant see what.)

Thank you for the anticipated help!!!