Thanks Jeff. I never heard that a top shouldn't be left down overnight. I'll be sure to put it up. The top goes down far enough. The alignment problem is left to right. The people I bought the car from said the top is only a year or so old. I thinking that the top installer probably didn't do a good job lining it up. However, I don't think the car ever saw a garage until it got to my house.
I found this link today. I may try to play around with the adjustments.
http://www.fordsunlimited.com/tech/Convertible.htm#table
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'73 Convertible, 351C 2V
'91 LX Convertible 5.0
Member: Valley Forge Mustang Club