So basically my engine took a crap and I bought a "used with good compression" engine off of ebay. I snatched the old one out and got this one in with no problems in a couple hours. Replaced the oil and put new coolant in it. When I go to crank it, it just turns and turns and turns. It turns kinda slow?? to me compared to the old engine. If I give it gas and crank for a few seconds it does the same thing but sounds like it wants to start and I can hear pressure coming out of the exhaust. But thats all it will do. So with that being said, I have:

-changed the plugs (checked plugs after cranking and all look good with a little fuel on them except the one in cylinder 3 which was black)
-checked all electrical connections
-tightened down carbs and air box (took it off and put it back on about 5 times)
-choke cable is fine and adjusted right
-checked spark and im getting blue spark on all 4
---> I WILL go to autozone in a little bit and rent the compression tester kit to verify this

Other notable things I noticed:
-Sometimes when cranking, white smoke will puff out of the exhaust but it is hardly noticeable and it only does it sometimes
-I tried to check the timing but the gear has none of the timing marks on it (timing advance maybe)
-backfires sometimes

What could this be?

 

kinda sounds like you have your firing order is off.

sitting on the bike the left most cylinder is #1 > 2 > 3 > 4

BUT the firing order is 1-2-4-3

each coil fires 2 plugs at the same time 1&4 and 2&3. Depending on which of those 2 is @ compression, the other is what is called a "wasted spark."

In factory configuration, the coil on the right is for 1 & 4, the left for 2 & 3. Also - the wiring harness going to each coil has to be hooked up to the proper one. Yellow w/blue stripe is the 1&4 coil. Blue w/ Yellow stripe is for the 2&3 coil.

check all of that if you haven't already.

 

All of that has been checked and checked again and I just verified it again. What else could it possibly be?

 

So it turns slow? That sounds like your battery might be cooked, or that there's a bad connection somewhere, or your starter relay is going a bit. You did say you've taken a look at all of those, so I'll assume that's all good. The starter could be done, but that's quite unlikely, the starter on this bike is pretty bulletproof. The starter clutch or idler gear could be tweaked, but hopefully that's not the case. Lightening striking the same place twice isn't unheard of, but it sure sucks when it happens!

What pilot settings do you have? Are the carbs clean? Are the carbs at least visually balanced? Are all the vacuum ports on the block (air injection on the exhaust side, carb synch ports on intake side) blocked off or connected to the emissions hardware they should be connected to? I doubt your crank position sensor is off or the CDI is busted. You only need fuel (air/gasoline), spark and timing to get it going, but if anything is wildly off you're going nowhere fast. Any of these one things being off (except the electrical stuff) will let you run if poorly. But if you get two or more going together, specially with slow turnover, and it just won't fire.

Have you tried bumping it? That'll usually start up stubborn starters when the motor wont turn over fast.

 

Well here's the deal, I could bump start the old engine but I was sick of doing so. It ran good, so I know my carbs are in good shape. I simply replaced the engine on my bike that ran fine already just didn't start with the button. Forgot to mention, the engine was dropped by ups and the oil pan and oil cooler case was cracked but I replaced those. Upon cranking, I can see the crankshaft spinning and cams and stuff so everything looks to functioning mechanically. The intake valves open and close as they should
All the ports right below the carbs are blocked off. Battery is good and fully charged. Maybe it's turning over normal and I think it sounds like that because it's been so long since I heard it start without bumping...

 

If you have an F2 fuel petcock, the vacuum port on carb #1 should be connected to it, not blocked (you said you blocked all four). Also, assuming your petcock is opened when you are doing your tests, is there fuel in the bowls when you open the drains?

 

plenty of fuel in the bowls, my petcock doesnt seem to be from an F2 because there is NO vac line, and it doesnt move from DOWN MIDDLE UP... mine is LEFT(on)UP(off)RIGHT(reserve)