Sounds strange that a carb issue would effect only certain cylinders, unless it was multiple carbs like on older motorcycles. If it's consistintly # 2+3 cylinders it may valve related, but you said you checked the action. Did you check for correct valve lash/clearences when you installed the head? 

Agreed, it does sound strange that the carb could do this(it has 1 double barrel carb), since both barrels dump into one bay that splits into all the  cylinders.  But I am trying anything, and the carb being cleaned couldn't hurt.  Yes, I adjusted the valves on the new head, after I installed it on the engine, then rechecked them after it had started running funky.  The rocker arms look like they are all moving fine to me as well, but I took a vid of them for you're entertainment, and maybe someone would see something I didn't: 

viper87 - MVI_3248.mp4

Could something like a rag have got sucked into the manifold and be blocking
the runner that feeds the rear cylinders? is the air filter in 1 piece?

Damn that's a clean head!

Ya, he just put it on, it better be clean.

In reference to my last post, where was the intake manifold kept while the truck
was apart waiting for the head? and how long was it apart?

Was anything stuffed into the intake to keep crud out during storage etc. ?

See where I'm going with this? you might have to pull the carb or the intake a visually
inspect for some sort of blockage if all else fails.

I know it sounds extreme, but if all you have told us is correct and you are sure there
aren't any bad plugs (junk new parts) and all the wires are good, the firing order is right
the compression is good, the distributor is not dropping spark on those 2 cylinders for
some strange reason (bad dizzy pickup) the valves are opening, no broken rockers, etc.
then it should run fine.

My $.02
Wild

For weird items, I have seen an EGR valve that is not functioning properly cause the number 3 cylinder to drop at low RPMs on two different vehicles.  No idea why it only effected the number 3.

Thanks for the replies guys! 
I took the Intake off, looked down it, and watched the intake valves move up and down in the head, free and clear no debris whatsoever.  I checked the timing again I think I'm doing it right: camshaft pulley mark at top, crankshaft pulley mark at 0 degrees, and distributor rotor pointing at #1 spark plug wire.  I am thinking it has to be something with the spark, but I saw each plug wire sparking... Could my new msd blaster 2 coil have been to powerful for the stock distributor and damaged it?(I didn't use the resistor like it said to, but the vehicle had a the same coil on it with no resistor for years).  If that was the case wouldn't it not be sparking at all, because if its still sparking, it should be igniting the fuel I would think.  Pics of the intake:

Seems strange to me why the #3 and #4 intake are cleanish, but the #1 and #2 intake are dirty/oily. Its the same on the new head.

#3 & #4 intake

Crank mark up, cam mark down, that's the factory way, but as long
as you have the timing right it will run, but the #1 plug wire will be
180* out from stock.

Stock is #1 is at approx 5 O'clock, yours with the cam in it's position
should be at about the 11 O'clock position, check the wire positions
and see if it's on the right way for your cam position

Mine is at about the 11oclock position like you said, I may try it your  the cam mark down and crank mark up way.  Right now however I am stuck on this carb, I took it off and forgot to note how the linkages go or take pics, can you help me out?  I'm not sure how the top and bottom links connect, or if they even do.  Does anyone know?