2000 T/C won't turn over

Just did work on 2000 T/C but battery was too weak to turn van over adequately. Tried to jump start the van but the jumper cables were connected to dead battery backwards. Realized they were backwards after no response when turning the key and seeing smoke...about 3-5 seconds. Now the van won't even turn over. Checked fuses and wires, find nothing wrong. Got new battery but still won't turn with ignition key turning. I have power to main starter lead but nothing through small selenoid lead. Tried jumper wire straight to starter selenoid terminal and engine will turn over, but won't start. All fuses and relays check out good. While trying to diagnose the problem found out alarm system chirps like it is activating, but no dash light flashing. Everything works with key in on position but starter, no selenoid click or anything. Oh, yeah, I also had the starter checked at the local automotive store and it passed. Did I fry the anti-theft system or something else. Please help.

Just did work on 2000 T/C but battery was too weak to turn van over adequately. Tried to jump start the van but the jumper cables were connected to dead battery backwards. Realized they were backwards after no response when turning the key and seeing smoke...about 3-5 seconds. Now the van won't even turn over. Checked fuses and wires, find nothing wrong. Got new battery but still won't turn with ignition key turning. I have power to main starter lead but nothing through small selenoid lead. Tried jumper wire straight to starter selenoid terminal and engine will turn over, but won't start. All fuses and relays check out good. While trying to diagnose the problem found out alarm system chirps like it is activating, but no dash light flashing. Everything works with key in on position but starter, no selenoid click or anything. Oh, yeah, I also had the starter checked at the local automotive store and it passed. Did I fry the anti-theft system or something else. Please help.
Where in the engine compartment did you see the smoke coming from?

Believe it or not, just the battery terminals....UPDATE: I checked continuity of selenoid lead from fuse/relay box and all was good. Bypassed starter relay by using jump wire from positive starter relay terminal to selenoid and got engine to turn by turning ignition key, however getting no spark. Tested all relays and had to replace one then retired for the night. Today after reconnecting the battery, got no horn and can't bypass relay to get the engine to turn over like last night. The "Motor Light Truck & Van Repair Manual" I'm using has no section for the security system.

I think I would take out the new battery and charge it fully so there is no doubt there. Then if you are able, determine if there is a large draw with the ignition off and all lights including dome lights etc. off too. That should tell you if something is now shorted. I would then see if anything works in the accessory position of the switch, radio, wipers, rear vent windows, locks, windows,etc. That should tell you if the BCM is awake at least. If you can't get that far, I would find out why, before you go much further jumpering etc. If you jumper the wrong things you can fry Inputs and Outputs of the PCM/BCMs.