Team. take it from an oooold techie, loose the WD-40 it's a penetrating oil. Try a product called Super Lub made buy Synco out of Bohemia N.Y. It's a teflon based synthetic available from U.A.P. or other auto parts distributers, in a spray or grease.
The squeek or grinding from the doors is common in all the Stangs and is a SOB to get rid of. I use a hypodermic filled with a reduced consistancy grease (mix the grease with the spray in the hypo) so it flows through the needle and lub the rubber bushings in the suspension to get rid of that noise from under the car as you've described. The synthetic won't hurt the rubber.
Hope this solves the promlem.
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99/ Silver GT 4.6 SOHC
M.S. headers 3.27
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