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I’m going to have my 2005 Jeep Wrangler’s software updated, will this help or hurt?

Had a 92 ford mustang 2.3L changed engine to the 5.0. After the engine change I noticed that the check engine and air bag light is flashing. Has anyone had this problem, what may be the cause? I read somewhere that it could be a module. What could it be, looking for specifics without having to take my engine apart again. Thank You.

my 95 intrepid is in limp mode. I have checked a few things and found there is no power coming off a light green wire at the trans controle module. That is the 12volt supply wire i checked this on a wiring diagram. Could this be a computer problem. I am able to apply voltage to this wire using a jumper from the battery and i can here the relay clicking on but still no shifting.