Once you get the tire mounted on the rim and the bead is set you have to let the air back out of it then slide it up into position, mount it back on the bike tighten everything down and then re-air. Hope this helps.
What has already been said surely helps...I tend to lower the bike on to the wheel (dropped my CT 3 times now). Having someone to steady the bike also helps as you tug and pull. Once you get the wheel semi in place...have the helper put in the axle part way while you hold the wheel up (you can do this yourself...but it is a balancing act as I use my foot to hold the tire up). Once the axle is in part way...this takes the weight off of you holding it up. Then you can put in the brakes etc. an be able to thread the axle the rest of the way. Good luck. It is a pain...
If you are still using the stock mounting with those pipes you also might want to reverse the mounting bolts so the threaded part is to the outside and bolt head inside for more clearance.