So today I jacked up the bike and checked the shift linkage...hoping for an obvious sign to explain my clutch issues. No such luck. The linkage looks brand new. I removed the rod and checked it carefully...it's fine. When I put it all back I did lower the shifter a bit. It was always too high for my tastes. Nothing was loose or worn or bent anywhere.

Can someone tell me, if on this particular beast, you should be able to shift into any of the five gears while the engine is running and the bike is standing still? I seem to remember being able to go at least from N to 1st, to 2nd and into 3rd, then back down again with zero issues when I first got the bike. I could also be confusing the Honda with the Savage (havent rode the Nighthawk in a couple weeks...doing a handlebars/controls/cables change).

Getting a bit frustrated with this thing to be honest. 4000 miles, any bike ought to run like new. I didnt take the clutch side cover off, did nothing but a couple of oil changes and played with the cable (and today adjusted the shifter linkage). I've also developed a rattle in the tank/speedo area...probably due to messing with the tank mounts when I installed the S40 seat (I used the rubber cork seat riser method).

I know the bike is "finicky". I have the idle correct, the right oil in her at the correct fill level, and have adjusted the clutch in every way that the manual calls out. Nada. Still, goes into 1st only if I give the bike a tiny foot-push (or move the clutch lever back and forth about 3/8"sometimes works), and will not go into 2nd from neutral no matter what I do if I'm standing still and idling. Again, once moving she seems to shift clean...both up and down.

I'm at a loss.

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In that case, you may not actually have anything wrong. It isn't unusual for a motorcycle transmission to be reluctant to shift if the wheels are not moving and the gears aren't turning.

If you just ease the clutch out to the beginning of the friction zone then pull in, and press the shifter which ever way you want.
You can shift with it not running. Rock the bike.

Earbuds make the world a better place when riding the LS650.

OMG, what kind of 14th century monster did I buy?  

What Kenny said sounds about right....it feels like the clutch isnt breaking loose. I dont know what I could have done to it to cause it to act that way. It didnt give me this problem before I changed the clutch perch/removed clutch cable, and did the 2 oil changes in quick succession. When I do what Kenny suggested I can shift quite easily into first. The idea that I would have to do that every time I ride is not compatible with my idea of bike ownership.

Possible that the previous owner used a synth oil and the bike is just "getting used to" the Rotella T?

Just sit on it, get it in neutral, move it a coupla inches,,
See how that acts,, if it's not enough, next time, get more involved.

If just moving inches doesn't do it, next time, try more, till you discover the least amount of effort required to accomplish the goal.
That may change as the weather cools. I never had the problem, just fired up in neutral and dropped in first. Yeah, there was a bit of clash, but those gears are plenty tough. All they are fighting is their own momentum and the shear strength of the oil stuck in the clutch.
If it's warmed up and you're sitting in neutral at a light and holding the clutch lever in, the gears can stop and it won't be easy to get in gear if they stop where they clash, just ease out to about where you would feel the clutch start to pull away from a stop, pull back in, drop in gear. I've run a bike through all the gears sitting still, just let out on the lever enough to just touch the beginning of the friction zone.
I stalled in traffic in fifth gear, unfunny , stupid moment, but it can be done and quickly.
The lever adjustment, lowering it, good plan, that should make getting second easier. A slightly bent rod will flex on down shift, a serious bend would lower the toe end of the lever and flex some both ways, but a vigorous shift action should get it in.
I'd go ride it, like I was drag racing. I mean get after it. Run that dude up in first till the rate of acceleration starts to drop off a little, slap the gas off, grab the clutch and shift it like ya mean it. Might not drop the clutch lever and wring the gas full on, if you Didn't get the shift, don't wanna rap it out, but that Should work. Then play with it, learn the minimum effort. I've shifted to second without the clutch, it's too big of an RPM jump for me to master it and make it smooth, but second and up, the bike will shift, quickl, smoothly and without harm, upshifting and downshifting. It's just a matter of timing and technique.
And sometimes, it's just gonna klunk a little dropping into first,

In time you'll tame the beast. It'll do what you want, when you want.
It's not broken or bad, you're just not speaking its language yet.