Thank you Ted!  I turned 27....awfully close to 30...feeling old  
 
We got the motor mounts finished up, adjusted the CDI mount location, moved a pipe mount, and made a new pipe mount.  My dad re-created the KDX frame hoops at work yesterday, plan to get those on one day this week.  After that I can tear down and start powder coating it.  The plate we used for the mounts was a bit heavier than I wanted to use, but it was free so I can't complain.  As long as the welder knows where to focus the heat, shouldn't be an issue (I had a pretty good welder on my side lol 30+ years experience).
I also was a bit unsure about my wheels, being the first time that I ever actually laced and trued a set.  So I broke down and got one of those spoke torque wrenches.  I can now confidently say that all of the spokes are at least 40 in-lbs, the wheels have .020" or less runout in all directions, and they should be ready for tires  
 
Here are some photos... I have some questions about some things I ran into, please see the bottom:
1. The coolant line that exits just above the motor on the right side.  Any good ideas how to address this?  I ended up using the KX hose right off of the radiator, then spliced into the KDX hose about halfway down.  I don't have any photos, but it seems to fit nicely when the pipe is on and everything.  I didn't know if I could use a complete hose off of something else here?
2. With everything together, the silencer doesn't fit completely into the pipe.  Is there a way to create a reliable seal between the silence and pipe without having full engagement?  Or should I be looking at modifying the mounts for the silencer?  I am using an 05 KX250 silencer.  I was thinking about making a plate out of aluminum to offset the mounting pipe mounting holes further back, allowing for full engagement between the two pieces.  
3. For the lower pipe mount, we welded a tab onto the frame.  The plan was to run a bolt thru the pipe tab and into the tab on the frame, meaning the bolt would go straight across, horizontally.  I planned to put a piece of rubber hose over the bolt between the two tabs to allow it to absorb some vibration.  Am I asking for trouble having a pipe mount like this?  I know that all of the factory mounts have those rubber hangers that allow the pipe to "hang" rather than be bolted straight to something.  I don't know if I am explaining it well enough, hopefully the photos will help to explain better.  I wanted to re-use the factory style pipe hanger there but couldn't get a spot for the tab on the frame where that wouldn't interfere with the pipe.
4. I wanted to run the KX125 kicker.  It looks like that is going to interfere with the pipe too much, so I ditched that idea.  I hate the KDX kicker, so that is my last resort.  I got a KX250 kicker and it almost works, just wants to hit the frame a little when its turned in.  Anyone else deal with that?  It doesn't seem like that big of a deal, I was thinking about putting a piece of rubber hose on the corner of the lever where it contacts the frame.  Then wrap it up real good with some self fusing tape, should isolate the vibration?
I think those are my biggest concerns at this point that I would like to try to figure out this week before starting to prep for powder.  Any input you could provide would be much appreciated!