I just cleaned out my carburetor and replaced most of the gaskets in it. I did not remove the jets but I did spray every passage I could find with carb cleaner and blasted them out with compressed air. I replaced the float needle and seat and adjusted the float level by bench testing the carb with a fuel jug and some fuel line.

I just reinstalled the carb into the samurai and now it acts as if it is getting no gas whatsoever. I looked in the float window and the fuel level is right at the white dot on the glass. The engine fires right up on starting fluid but I can't keep it running. I can give it throttle  but as soon as it runs out of starting fluid it shuts off as if  it had a kill switch.

I'm stumped at this point. Did I do something really wrong when I reassembled the carb?

My bet would be it is a carb problem.  You either didn't put something back together right, or some crap got loosened up and clogged up a fuel passage.  I suppose you could have put a vacuum hose on wrong too.  Or there is a vacuum hose that is leaking and causing it not to run right.
After you replace all the vacuum hoses and make sure they are all connected correctly (if the problem is still there), pull the carb and start checking for other issues.

Do You Have the Hatachi OEM Carb?
Make sure you have all the Plugs in the right places, (They are keyed, should not have crossed)
The important one from your description, is the "Fuel Solenoid & Metering Valve". It has 2 wires that come out of
center & top of the Carb, They hook up to the Tube looking thing with the O-ring that seals into the fuel bowl floor.
If this doesn't "Turn On" (open) your main jets won't get any fuel.

Just a shot.......

CAPT

I forgot to mention this is a stock hitachi carb. I'm going to go test the MCS and Fuel cutoff as soon as I get a chance

I tested the fuel cutoff, IT pops the needle back and forth, I put it back in and again verified that it clicks when I turn the ignition back on. I again looked in the float window and I can slosh the gas back and forth when I rock this vehicle back and forth. I tried starting it without the Fuel cutoff needle installed and again it's like there is no gas at all. I can't even smell gas in the carb. I even tried jamming a rag in the carburetor to force it to go rich and again, nothing. I tried pumping the accelerator pump piston by hand and nothing came out the nozzle.

Explain this one to me, When bench testing this carb I had to reset the float level to 20mm which is also where the previous owner had it. When bench testing and accidentally flooding this carb I could pump the accelerator pump and see two streams squirt out the accelerator pump nozzle. Now that I have the float set at 20 mm which brings the fuel level to the middle of the sight glass this carb acts like there is no gas at all in any passage or the accelerator pump. Now When I pump the accelerator pump by hand I can hear it bubbling like gas is in there but I can't get any gas to squirt out the nozzle in the throttle bore.

Again I am stumped. This carb kinda ran before I did this. it idled fast and rough and the Samurai died on modest acceleration.

At this point I have a second carb from the junkyard and I am going to order another gasket set and try again.

There are some tiny springs and balls that go into various passages on the carb.  If you would not get some of these put back in, or put in right, then that could cause some issues.  I still say you either didn't get the carb put back together correctly, or there is some crud plugging something up.

Ok, I am not taking any chances with this second carburetor. So far it appears to be in better shape than the one on my samurai now. Also, the float level was set a 10mm which is closer to stock. SO i got a good feeling about the float on this one. I am taking this one farther appart than the previous one and I am going to boil it in 10:1 distilled water and lemon juice for 30 min. I am going to carefully look at each gasket and make sure every fuel and air passage gets an appropriate hole in the new gaskets to go through. I want this one to be surgically clean and tuned as best as I can before I put it on.

The question I have is, would it be ok to boil the Mixture control solenoid in my solution because the MCS is a pain to remove. Otherwise I am going to clean the upper carb horn with WD40 and carb cleaner spray and compressed air.

If it were me, I wouldn't soak any electrical component in liquid.
No matter how you clean it, you should blow compressed air through all the passages, to ensure they are clear.

confirm that the float bowl is really half full by removing the carb top (while it's still on the truck). The site glass may be wetted out with cleaner or WD40, giving you a false reading.

If my suspicion is correct, the float bowl isn't getting filled properly. Either the needle is stuck closed, mis-adjusted, the float is in a bind, or you have no line pressure from the fuel pump.

Fuel line pressure: crank the engine over with the fuel line disconected at the carb, into a clear plastic water bottle or soda can w/top cut off, to make sure the fuel pump is working. Make sure the fuel looks and smells right. Cranking the engine over with the starter should push a teaspoon of gas with every revolution of the engine, every pulse of the diaphragm fuel pump. If it doesn't, start by checking for a clogged filter near the fuel tank, then the fuel pump itself.

Don't blow compressed air into the carb fuel line inlet, you'll mess up the float height by bending the float tang.