I like your planned "checks", each makes sense, David...
Backing this up just a bit, let's rule out any engine assembly related stuff. You were attuned to the video during cylinder and head engine assembly. As I noted in the earlier reply, I walk the viewer carefully through the cylinder head nut tightening sequence and repeatedly use the reference "49 ft-lbs" final torque, even citing four recommended ft-lbs torque steps as you bring these nuts up to full torque, then a recommended recheck twice at the 49 ft-lbs. (All of this is between minutes 14 and 17 in the rental video.) If you followed these focused steps, the torque should be right, and you're past any concerns about the engine compression seal and air-fuel mixture dilution from a seeping head gasket. On that same note, the valve timing chain tensioner was presumably in good condition and should have tensioned the chain properly after installation. This would assure proper valve timing and chain tension.
If the engine is sealing properly, you're on the right track at the carburetor. If fuel volume to the carburetor is adequate, there are two concerns here. You reset the float, and that's a big one, as the float level must be high enough to keep fuel flowing sufficiently and not so high that there is flooding or spilling of fuel out the overflow vent tubes. Set properly, the float level will not seep fuel with the carburetor leaning moderately, like when the bike is on its kickstand.
So let's move to the carburetor idle pilot screw adjustment. Yes, you have the installation sequence correct: O-ring, washer, spring then screw. To clarify, this pilot screw is a fuel supply screw, meaning that as you screw it out or open it, more fuel flows into the air stream of the carburetor. If the engine ran with this pilot jet screwed in all the way, it's obviously getting fuel from somewhere. Before looking for an internal fuel leak (high float level, seepage past a passageway or casting, etc.), make sure the choke is opening completely. Find a stable idle point with the cable connected idle stop screw, even if the speed is somewhat fast. Now turn the pilot jet screw inward and out to see if that has any effect on idle speed.
If the engine won't idle down with the idle speed screw setting, usually it's not getting enough fuel. If it races and won't slow, its getting too much fuel/air combined. Extra air can be an air leak between the manifold and head or manifold and carburetor, and this would raise idle speed. Engine running (as slow as it is capable), take your WD40 and carefully spray around the intake (rubber) manifold with the engine speed as stable as possible. (Avoid spraying hot surfaces like the exhaust system, you don't want to set yourself, the bike or the garage on fire! A fine mist is all you should need, vacuum will pull the WD40 into the intake stream and change the engine speed.) If you hear a change in engine speed, there is a manifold or attachment point leak. Correct this.
Note: To rule out cylinder head gasket seepage, with the engine running, spray a fine mist at the head gasket mating point around the cylinder barrel and head. Again, avoid the exhaust heat and risk of igniting the WD40.
Other sources of air leaks can be the carburetor slide cover or the cut-off valve cover and port seal. Check these areas with WD40 mist, too. If there is an air leak, little fuel from the pilot jet may be enough to increase engine speed and give a "false" idle setting. Eliminate any and all external air leaks, beginning at the air box to carburetor inlet (to protect the engine from dust seepage) to the cylinder head.
Also, I would check for a throttle shaft leak, another point where air can enter from the outside. Visualize idle mixture as dependent on air only coming from the correct sources within the carburetor. Rule out slide to bore wear, which can also throw off the air flow—here, too much air seeps between the carburetor slide bore and the slide. Slide and bore wear was a notorious leak point on vintage British Amal carburetors, the Concentric type in particular. The engine would warm up, and the idle speed would creep up. There was a ready source of air and a fuel supply.
The slow jet and main jet should not be involved in the base idle speed and mixture issue. (You're using the OEM Euro slow jet, a 65, right? I'm running a higher flow 68 at 4400 feet elevation with no issues around adjusting the idle mixture.) Needle height should not be an issue, Euro OE clip position is 3rd groove from top, same place I'm using. Make sure the needle clip seats properly at the top of the slide. Be sure the needle seat is in proper position...If the engine idles at normal operating speed warm (around 1400 rpm) with the pilot screw turned in all the way, the carburetor is supplying fuel from somewhere. If the engine won't idle down to 1400-1500 rpm, it needs either air or fuel, or both—there's either an air restriction or a fuel restriction.
David, here are some helpful PDFs, a carburetor schematic and the factory steps for setting the pilot jet screw. Zoom-in for details on the schematic. Account for all of the parts within the carburetor:
Honda XR650R Keihin Carburetor Schematic.pdf.bmp 6.35MB
Honda XR650R Keihin Pilot Jet Adjustment.pdf 230.03KB