When the battery was dead on 2006 ultra classic I pulled battery to charge it when I reinstalled the battery the bike will not start only the security light red key comes on What did I do wrong?

Look at the fuses in under the two side covers. The same thing happened to me. It blew the ecm fuse on one side and the ignition fuse on the left side.
The shops said I had set the bike alarm and I needed to turn it off or replace it. I don't have one. Abbie was instrumental in helping me, The service tech at Jim's Harley D in St. Petersburg Florida knew what was wrong, he talked me right to the problem. He knew how to diag. from the odometer computer, gave him the error code and we checked a couple of things... secure connections, went to the fuse and bamm. Replace a couple of .50 fuses and I'm back in the saddle again. Jim's Harley-Davidson Shop came through for me and he did not charge me a thing, in fact he said thanks for calling!

Tom Kosharek
Largo, FL