This sucks, I had a long post that I was typing and the page I was typing it in crapped out so this is going to be a shorter version.
Took it into the shop and they basically charged me an arm and a leg for a "restore". Told them that I would only want them to take a look at the jetting instead of the full list of items they recommended and they declined. What a waste of my time!
Anyway, the lesson here is that if you are working on your bike and your bike is your baby then you should treat it as such. No one else is going to know it as much as you.
What I'm going to do from here is try to fix it myself. So let's revisit what's happening...
The bike idles fine. As soon as it's warmed up i take it out for a ride, drop it into first and disengage the clutch slowly. While riding the friction zone on first and twisting the throttle about 1/3rd of the way the bike sounds like it's struggling. RPMS are around 3k and it starts to take off very slowly. I get to around 15 MPH and it still sounds like struggling to get speed. I shift into 2nd gear, disengage the clutch and now it does the same with 2nd although now it feels like it's gaining some speed. If I twist the throttle more and more the RPMS shoot up and the bike slowly start going faster. It definitely sounds a little healthier and it starts picking up speed. Since it's a brand new engine and new rebuild I don't push it any more. I take it around the block a few times and it's the same. Whenever I come to a stop sign it dies sometimes as well. I have to keep revving the engine for it to stay running.
So those are the issues I've been experiencing. What I'm going to do from here is switch out the Open Kerker exhaust and install my old stock cb750F SS 4-2-1 exhaust. I'll take it around the block and see how it runs. If it runs better, like it did before I installed the new exhaust, then that means it's probably a jetting issue. If that's the case then the next steps would be to buy a bunch of different size carb jets that are higher than my stock (105 Main and 35 Slow/Pilot). Does that sound about right? Am I heading in the right direction? I'll update everyone with what happens.