righto.. from them pics it looks like the timing is miles out, you say it was still running b4 u stripped it down so i hazard a guess that its jumped since....
My advice is to remove the plugs, remove the cam chain completly and align all the marks to where they shud be, like i described in one of my replys above.
Hopefully it shud all line up and you can carry on with ure replacement.
when it is all back together, and tensioned up then you can rotaate it by hand too see if it rotates ok, if it still locks up , then you may have to remove the head and check for valve/guide/ piston damage..
How the marks shud be..





And if ure replacing the balnce chain to

hope this helps