Oh, and there definately is a little pride in being able to take something that several other people have had their fingers in without success and being able to bring it back to life.  

Finally got a little time to work on the bike tonight. I had taken the shifter cover off the other night but didn't see anything obvious and the gears were lined up properly. So tonight the first thing I did was slide the shift arm on the shift shaft and see if I could shift through all the gears: it would only shift up one gear into second and back into neutral, not down to first. It may be I didn't have enough leverage since it would shift into 3 or 4th either, not sure. Next I went ahead and dissembled the cam drive gear and shift pawl assembly, still nothing obvious.
Just a note, if you're ever taking this apart, be very careful taking the shift pawl assembly out. Use two hands if necessary and hold the pawls in place and be prepared to catch the pins, springs, and pawls because they have spring tension on them and like to fly in opposite directions.  . Also, zip lock baggies are real handy for keeping those tiny parts from disappearing. All that's left now is the stopper plate and the stopper arm. I left the stopper arm in and just removed it's spring so it wouldn't be in the way and then removed the stopper plate. Still nothing obvious.
So I tried putting the bolt back into the end of the shift drum to have something to try to turn it with and try to shift through the gears. Seems to move fairly easily but the shift drum moved out a little and that made me a little nervous as I really didn't want anything inside the Trans to come apart. Probably wouldn't but I wasn't going to take the chance. I was able to get the shift drum to neutral and made sure the stopper plate lined up with stopper arm in the neutral position. Then I put the cam driven gear and the shift pawl assembly back on and tightened the bolt. Now the shift pawl assembly has flats on it that I could put a large crescent wrench on and that gave me a little leverage to be able to move the assembly and shift through the gears. Again shifted into 2nd and back to neutral easily, I could feel it shift and turning the output shaft verified it was in gear. Tried up shifting again and got it into 3rd and 4th by rotating the output shaft a little, and shifted back to neutral. Tried 1st again and with a little fiddling with turning the output shaft while trying to shift it finally went into first! Yay!
Shifted all the way up to fourth and back down to first pretty easily a couple times. So I know first gear works, I'm just not sure why it didnt? There's a couple possibilities, 1, something was jammed and playing around with it got it come loose. 2, it was assemble wrong, even though I didn't see anything obvious I'm not familiar enough with it to say positively that wasn't the case. I don't think I had taken the shifter cam gear and pawl assemblies apart before but I did take the cover and shift shaft out to replace the seal and paint the cover so it's possible, it was almost two years ago now! Lol! And the third possibility is simply that I didn't get the linkage lined up right when I put all back together in the frame. I think that's most likely as the shifter arm was not straight down and Verslagen said it should be back at the beginning of this post. Also, after rechecking my Clymer manual I realized I had the arm on backwards, meaning the linkage was to the outside of the arm where Clymer shows it to the inside. I really didn't think that would make a difference as long as it moved the shift shaft properly but I've been known to be wrong once or twice.
So that's where it's at now. Putting the cover back on tomorrow and my stator should be here tomorrow so I can put the rest of it back together and see if I have any success with it.
Sorry again for the long post but hope it helps someone if they have a similar issue.
Further updates coming once I get everything back together.  

Ok, thanks for the info Dave. I'll keep that in mind when I get her back together.

If the bike's not running I would just push it forward to shift the gears as your starter gears will not like backing!

Finally got the bike back together, shifter and linkage set up right, new stator installed, and new air intake/filter setup all installed and switched to Rotella T5 15w 40 oil. Oh, and rejected the carb while everything was apart. Phew, what busy couple weeks! Lol. Fired it up, checked my oil level and was finally able to see through the sight glass properly, it was good to go! Road down the road, 1st, 2nd, 3rd, 4rd, great! Tried to downshift when coming to a stop, got into 3rd and stuck there. Pulled off the side, played with shifter a bit and finally got it to shift down to 1st. Down the road again, still doesn't want to down shift. Off the road, played with shifter and got it into 1st again. This happened a couple more times till I finally got a feel for it and figured out that if I just lift the shifter slightly before I downshift from 3to 2 or 2 to 1 it shifts much better and pretty consistently. Doesn't seem to be any problem between 4 to 3. So I rode like for the night without too much more shifting problems. I'm thinking I probably need to adjust the shifter linkage some or the shifter return spring is getting week and not returning the shifter completely to the middle position. Now the question is do I need to lengthen the shift linkage or shorten it? I'm thinking since lifting the shifter slightly, which is pulling the shift arm forward,before shifting helps downshift that I should shorten the linkage slightly, which will pull the shift arm forward. I plan to tweak it some today and I'll let you know how it goes.