Although you already checked the engine and detected not a hint of imbalance... when there's a load on the engine there's a bit of a difference as to what's going on internally versus without a load and since you switched from Auto to Std the difference in weight from flex-plate/converter to flywheel/clutch-pack could be a consideration. More so, since it was sitting for 6 mos +/-, it might be worth checking out the vibration damper. If memory serves me, there's the inner and outer hubs which are bonded together by "rubber" there should be an alignment mark (a scribe line along the center going across both hubs) if the line isn't "lined-up" the rubber has failed and will no longer "effectively dampen" vibration changes. The other thing to look for (there might not be a scribed alignment mark) is just the condition of the rubber, IE: if it looks smooth, not cracked or bulged out (front or back sides - check with a mirror and flashlight) then it "should" be OK. However, if the hubs aren't aligned (even 1/32nd"), rubber is not smooth, is cracked and/or excessively bulged out it "could" provide unloaded dampening "but" everything changes with a load... Something else to look at. sorry, but you never know...
Not saying to go out and get a new damper or anything, but if it doesn't check out good this could be the gremlin. On mine at around 160k or so I found the damper rubber was cracked, brittle, bulged and (I'm almost certain) the scribe line was off by about an 1/8th", and there was no real indicator of imbalance at all. "But", when I installed the Fluidampr (at the time about $425 from Summit, Geno's now has them for 98.5 - 02 and 03 - 05 for $435 and for the 94 - 98's for $488) I immediately noticed the engine idled smoother and seemed to run quieter = a miracle.
Also, as mentioned by others here, when you have it up on 4 stands and can safely run it up to the speed where you're experiencing vibrations look at the propeller shaft carrier bearing. If, when at the speed where you've experienced vibration everything "seems" OK, remember there's no load on anything, try running it up and/or down in 5 mph increments. And "make certain" the universals are clocked/synced/aligned correctly from pinion thru to X-fer case flange. As for tires/wheels, if you've ever worked on bicycle tire/wheels and had to adjust the spokes to get the wobble out, when your tires are spinning look at the rim/wheel lips (inside & outside) for any slight variations - this is best observed while idling in gear - perhaps in your case 1st gear.
I hope you find whatever it is soon and it doesn't cost you a "BRAZILLION" dollars to rectify.