Not really vacuum FED... the vacuum supplied to the fuel tap moves a diaphram so fuel can flow to the carbs, using gravity...

 

Wait...if my 94 have a fuel pump, shouldn't a 93-99 all have fuel pump...chances are the PO did some mod...it's pre 92 gravity fed

 

Nope. Your 94 does have a fuel pump, but not the 98. Check it out...
Ronayers.com Microfiche Honda>Motorcycle>1998>CBR900RR>CARBURETOR ASSY

 

Yes, They stopped with the fuel pumps in 98/99.

Its' gravity fed with a typical vaccum controlled petcock for handsfree on/off operation.

 

+1 on pulling the Petcock out and checking the screen.

I simple test might be to switch it to reserve when the bikes stalls and see if that changes anything. Reserve opens another port on the petcock feed inside the tank. If that helps then you might have it.

 

Well I see what you're saying, and yes you are correct. Its just that in my mind, gravity feed involves a petcock with 3 positions: OFF/ON/PRIME, and the fuel flows without any need for vacuum.

But at least the OP has figured out his model specs!

 

I wonder if the OP found the problem yet...

 

Everyone... I've really learned a lot from this experience and the wide range of knowledge everyone has provide. But, this was problem and solution. Please remember one thing, I brought the bike this way and had to figure all this out when I was turning it back up.
1. Small vent hole at the bottom of gas tank was clogged all the way through the tank. Which we all know doesn't allow for the tank to breath probably. This was causing "Hydro-Lock", putting pressure on the needle springs and allowing fuel to flow into the cylinders.
2. Replace all 4 diaphragms in the carbs, they wasn't any holes in them, but just for safety precaution since the carbs were broken down.
3. Someone put a Stage 1 jet kit with the wrong springs placed back in the carbs. Springs were replaced.
4. Compression test was done, even across all four cylinders.
5. Petcock fuel pump was replaced. Carbs cleaned again for the third time, plus, were resynchronized.
6. New plugs and oil.
So...to some all this up, bike is running stronger, cleaner and 95% better. Just have to get a rear tire now (for the HP that's about to be pushed to the rear wheel), have a Yoshi to install coming in Saturday. Again, you guys have really been very helpful and educated me more. I'll be back with a picture post when it's all put back together.