Thanks for all your input. I installed the new transceiver. It mounts slightly different than the original, but works great. Antitheft lights then goes out immediately so the engine can start. No blinking Antitheft at all - and all three keys work like old times.
I appreciate all your help and advice.
In this case, an intermittent signal from the bad transceiver was making this problem tricky for me to diagnose. Fortunately, as you mentioned the transceiver can be removed and replaced with no programming. Very thankful.

 

For your consideration : The original 1999 transceiver in my truck was made in Canada and consisted of the plastic ring and the transceiver box connected by a flat section of rubber. Two parts made of plastic connected by a center section made of rubber. Perhaps this was to allow for the tilt column or for vibration. The halo portion is plastic with a thin silver foil ring on the underside. This appears to have been soldered to a very small wire which passes the signal through the flexible rubber center section to the transceiver box which is sealed. Mine is labled May 1 1999 Part number FB-15607-AC. The new transceiver from Ford is Made in Mexico and has the metal halo imbedded in plastic and is made of one molded rigid plastic piece with no rubber center section. The transceiver box is smaller and has two latches so it could be inspected internally (not sealed). The mounting is no longer directly under the column with the box, but to the side. The torx bolt fits differently, so you may have to put some English on the lower end of the plastic frame to get it to the hole and maneuver the works into position around the wiring bundle that exists there. It'll fit. The new part number for the Ford Part that I put in my truck is 1L3Z-15607-AA 1X ($125+ here in CA.) Wish it were easier to get around the PATS.

 

ProjectSHO89 - You are right there is more info on the European sites about Ford's PATS than there is in N.A. literature. There seem to be a lot of complaints about a 1:6 DTC that I looked at. I looked at a lot of online references and found a great DTC Fault Code Reading (from PATS LED) bulletin which I followed.
I know they don't mention it in the manual but I made a similar quick check adapter for the transceiver lower column connection by cutting the socket end and length of wires from my old transceiver. Now I can plug this in and probe the wires instead of trying to probe the tiny square sockets on the female end of the connector (hopefully). N.A. Ford should have mentioned the DTCs for reference somewhere, I would hope.

 

Day 2 with new transceiver.... Truck starts confidently over and over - every key works, my bootleg key, cloned key, the original key and the one which is cracked.
Lastly, I tried my last resort key - from Ace hardware - the $60 key that got soaking wet.... and.... All my keys work.
That bad transceiver truly made the theft light miserable with my 1999 F150. I'm happy with the new one I installed. It's faster and links quicker, I think. Ford changed the design and possibly fixed the problems in the design of the old one. I like the way it responds faster.
Now I feel less suspicious of the Theft light - since I tore my steering column apart, put it back together a couple times, checked everything twice, drank some cold beer on ice.

 

New Transceiver Swap Day 3. The transceiver works just as good as yesterday- engine starts vigorously.

 

Signing off. The new transceiver is working perfectly - every start.

 

thanks for having the same issue . I changed my trancever no luck . Computer is not handshaking ignition . Bought a doorman to report new ignition n keys only flashed red one time no luck. Mine did this ten days below zero then started now ten days rain no start. Pats is kicked in . Check ur voltage at mass air flow and