Slight mis-alignment on front wheel

Had to lay down the bike going about 10 mph when practicing some rear brake exercises, and afterwards noticed a slight mis-alignment in the steering. I have attempted to re-align the front end using several methods, and replaced the entire front end with my good spare set except for the front tire. The front tire also appears to have no damage or bends in it. Once the front end was replaced, I realigned everything following the usual methods.

After doing all this, the bike is still tracking slightly to the left so that I have to compensate with the handlebars tilted slightly to the right when going straight. The handlebars are in alignment with both the old and new upper triple tree, and do not have any bends. Are there any other potential reasons that would be causing this misalignment? Thanks in advance for any help.

Steering neck bent / twisted Check out looking at whole frame looking for breaks in paint or stress marks in tubing or gussets or bent tubes.
Rear wheel may have shifted / bad , loose bearings at swingarm pivot.
Place straight edge from side of front tire to side of rear tire looking for wheels to no longer being parallel.
Just some thing s to check.
Good Luck , Let us know
Dave

Checked the steering neck and frame, but seems to be no damage on a visual check. Held some pipes against either side of the front-end and they form a 90 deg angle to the ground when on the center stand, so seems to be very little if any bend in the front end to either side. Re-aligned the rear wheel (forgot to check, whoops!) and was off by a small amount, and fixing seemed to make the steering slightly better, but is still off a few degrees when riding straight.

I also checked movement of both wheels independently and they seem to move freely, and without any play or sticking of the brakes. If push comes to shove I can take the bike to my local guy that restores vintage bikes, but wanted to cover the basic/common stuff first.

How are you ( what method ) checking / installing fork tubes in triple trees ????
Dave

All clamps loosened, and first measured the height of the fork tubes in the upper triple tree as per factory manual, and then tighten down. Once upper triple tree height is set, then with the tire axle bolts, steering stem nut (& clamp), and lower triple tree clamps loosened and bike on center stand (on flat ground), I bounced up and down with weight on front to center the front. Once centered, I tightened up the lower tree and axle.

Basically this method for the alignment:

OK
Next wild guess to check
Fork oil / level
Front springs length and spring rates
Just trying to help you think out side the box
Dave

I'll check the fork oil level tomorrow, but just rebuilt the (backup) forks last weekend with new seals and oil. Both springs were within tolerance levels from book. Air PSI in both forks are 10 psi (within service level) from air gauge. I'll also measure the amount of inner fork visible from dust steal to lower triple tree, as I suppose that could show an issue if uneven.

Wondering perhaps if there's a bend in the rear tire or a spoke got loosened, as I didn't give that a thorough look...

I'd loosen one fork at the clamps and turn it to see if I could feel any binding then do the other side. Mine were just slightly bent but couldn't see it. New seals leaked until I twisted both of them to their neutral spot. Rode like that for years. Strate and true. In 13 when I put the bike back on the road I got new tubes, seals and progressive springs. I tried converting to air in my forks. Didn't work for SHT.
Steve

BTW, anything over 5 LBS the front end was hard as a rock.

About to head over to check the shocks. I had rebuilt them the other weekend and the inner forks roll flat on glass. Didn't feel any kinks when twisting around in the outer shocks, but could be wrong. It's just bizzare that the bike is still showing similar symptoms despite the new front end. I'm still not convinced on the rear alignment so will check that again. The front end was clearly out of alignment before but visually looks aligned now.

The one nice thing on the csr 650 is the presence of progressive springs and the air valves making them more adjustable, especially as I'm a bigger guy and need a tad more stiffness.

You are aware that the tires / wheels are not necessarily perfectly in the same line .
Rear wheels are commonly offset for chain / frame clearance
Dave

does the bike feel like it is falling off to the left or right when you try to go neutral on the handlebar grips.... as in almost let go of them?

Bent handlebars?