As RT325 said, if it was shifting fine before, adjustment should not have been needed.  All you need to do is "time" the gears...  should be punch marks to align. 

Anyway, fine tuning might have been needed...  just know that the trans won't shift without shafts turning so dogs can align with slots.  Don't fall into trap of adjusting because it doesn't want to shift while stationary.

I think I am getting too caught up in the fact that it doesn't always go into the next gear even though it appears that I have it adjusted correctly now: equal spacing on the fork to pick up the next cog. Hard to try and turn the shaft while shifting the lever. You are right the bike probably has to be running so everything is turning for the system to work properly. I will work on it again after work tonight and lt you all know.
Thanks for the advice. For sure I'll be an "expert" after this is all back together again!

You can push the bike while trying to shift it or spin the back wheel if in the air or spin the countershaft sprocket if chain is off.  It usually doesn't take a lot of rotation to get the next gear lined up.

When I get home tonight I am going to take RT325's advice and measure the throw of the shifter both up and down to make sure the gap between the shift fork and the pin is equal for both. That is what the Clymer manual is trying to tell me, but their method just won't work because you cannot measure that gap with a feeler gauge. So I will have my wife move the shifter up and down (slowly) and have her mark off on a vertical ruler when I start to see the shift fork engage the pin on the drum. When that distance is the same for both upshifts and downshifts (with the bike in 3rd or 4th gear) that is as good as it can possibly get. 
I try to rotate the rear wheel while moving the shifter up and down and success is spotty (hard to get the wife in the garage to help all the time!). But if the gaps are equal than the adjustment MUST be perfect. The manual calls out for a gap of 0.02" (if my memory serves me correct as I don't have the manual here at work) for both upshift and downshift forks. Let's see what I come up with tonight. Already prepped the wife that I will need her help. I think she actually hates the bike because it is so loud compared to the baby CL175  that I ride when she is out on her Honda Super Cub!

Did i say that. Must've been something like that. Not sure measurements are given on your model& i guess i mean't free movement by feel before it tries to change another gear up or down. The older models "68 250 & 360 up to "73 'without looking' gave a 20 thou measurement for the change arm thingy which doesn't relate to yours. But--i guess if you were in at the drum pin end & gear change was held fully up or down then there probably 'is' about that much gap between the claw arm & drum pin. Like--if you could grab the drum & turn it towards the claw it'll revolve a very little back to the claw. That's because the claw only pulls it 90% into gear. Think i said that today--maybe another post. Me loosing it i think. You should be able to sit on the bike & just move an inch or two forward or back if it wont change & should click through all the way to 5th doing that. Have a happy day & sorry if i ruined it.

Hi Guys,
Got it all back together after multiple measurements and adjustments. Oil is in and ready to start. BUT, it's dark and has been raining on and off so will wait until after work tomorrow for the test. The good part is that I'm done being pissed off at myself, and taking it all back down takes like 20 minutes so not a real big deal.

Funny, here is a little story for you. When I lived in Cali my buddy and I assembled and installed a new smallblock in his 1965 Chevy pickup. Beautiful truck. About 4pm on Saturday (after like the 4th weekend in a row working on it) and it's ready to start up! My buddy Brad says, "well, time to grab a beer and sit back and look at it". And I said "no, we are 99% of the way there, let's give it a shot and maybe take it for a drive". Brad, an older and wiser man than me replies, "Roland, it doesn't get any better than this right now. It can only go downhill from here". And you know, he was right! We got it running the next day, but it wasn't a piece of cake. We installed the distributor off by a tooth so it wouldn't start, etc etc.
So, that is ANOTHER reason (excuse?) why I'm typing this and not back out in the garage kicking it over!
I'll keep you all posted, and thanks again!!!

Good story. Look forward to tomorrows episode & hopefully good news.

Well, just closed the garage door, and I know most of you probably skipped work because the suspense was just killing you! But the bike shifts perfectly! So happy now!! Still have a leak, but that appears to be coming from that black plug right next to the shifter, which I have on order.
Thanks to everyone for your help!

Congratulations!!! 

Great job...  adjusting those shifters is not one of my favorite things to do.

Just came back from a short ride. Love the way it shifts! Now gotta solve those pesky leaks!