Yeah I had this problem on my truck too. I did the drivers side first and noticed the pin was like two inches in front of the hole. I just put the floor jack under the axle and cranked it up till it popped in. If you watch, as the spring compresses, the shackle moves backwards. On the passenger side, it was even farther off, so I put jackstands under the frame and jacked the axle up to just under the spring. Then I pulled the axle forward (by hand) until the pin popped into the hole in the perch. The jack needs to have wheels to do this. I just assume that they dont line up because they are loaded differently in a explorer/vs a bronco ii, and need to "settle" before they fit exactly right. I put in one inch blocks a few months after the swap, and I didn't have any problems getting the pin to line up in the perch hole.