ok, had mondeos for years and done loads of arms,there is no problem with putting the bolt in upside down, if as fiddy has said, you cut a few threads off first.. just check a mk5/6 escort there bolts are upside down from the factory!!
I have seen marks on casings where the bolt has his but not puctured through..

As for this issue, it could be that with the tugging trying to get the ball joint in, one of the bearings in the tripod joints has fallen off, happened to me on the wifes mk3 a few months ago when I changed a front spring, luckily I spotted it before I put it al back together..
thats my guess anyway..

steve