need some help here!!

[SPEEDY88]

I had a high flow x-pipe installed in my 96 gt. I had this done last week, and I took it to the shop to have a ding fixed on the left front quarter panel because my wife backed into my truck. Now, the check engine light is on and the "overdrive" light flashes on and off in the instrument cluster. I also saw that the speedometer doesn't work sometimes. I left the car on for a while and now it works but the "check engine" light is on. I know I have to install the MIL eliminators to get rid of that, but My question is why did the "OD" button flash and the speedometer stop working for a short period of time? Has anyone encountered this? I need to know what to do. IS INSTALLING THE HIGH FLOW X-PIPE BAD, CAN THIS VOID MY WARRANTY?