When security system activates do you loose power to windows and locks radio

I am no professional but logic would tell me that by replacing your ignition swith with most electronic security systems in place is like telling the security system to disable the electronics to drive this car away. Your security system might just be reacting to a security breach. This I believe is a perfectly normal reaction trying to keep your car from being stolen thinking a theif is taking your possesion. The question I have is why did you replace the ignition? Either way you could have the wrong switch or you will need a qualified tech to reset the ignition. This is a great way to learn that when you have security like this on your auto, it actually works.