So from what you have written you have a new key that works in the doors and goes into the ignition (and physically turns) but the engine will not start?
The red light on the dash may be blinking really fast, if so i think this is to show the alarm was set off. this should go out when you turn on the ignition.
IF your OLD key is chipped you should just be able to hold the OLD key up very close to the new key when inserted into the ignition and the senor in the column should read the chip from the OLD key, so when you turn the new key in the ignition the car should start.
again this is bases on assumption that you have a physical key that will work the locks now.
99 DII. CDL from a DI. 3" OME lift. 275/65/16 Duratracks 9k Superwinch etc etc