You put your thread in a forum specifically for people who have tuning questions about things like injectors, MAFs and aftermarket tuners such as Tweecer, Moates or Anderson PMS. Therefore you post will not been seen by people who may have an answer but do not visit the Tuner forum. Convertible top problems have nothing to do with tuning an engine.
My advice to you is to twofold:
1.) Send a PM to one of the moderators and have your thread moved to 5.0 Tech
2.) Next time you start a thread, think about where it goes. If you are new to Stangnet, please read the terms of service and give extra thought to where your new thread belongs. There is some help in the text below to help you find the best place to start your thread.
Tuning problems go in 5.0 Tuning, with specific emphasis on modifications to the injectors, MAF and computer, along with aftermarket tuners such as Tweecer, Moates or Anderson PMS.
General tech problems go in 5.0 Tech. Tech is for
suspension, electrical, brakes, body, engine repair and general troubleshooting on the computer & trouble codes
Tall tales about your 5.0 Mustang, pictures of your 5.0 Mustang project and stories about your last trip to the race track go in 5.0 Talk.
Do this and you'll get the best answers quicker and not get lost in the maze of posts about everything but the type of problem you are having.
Having said that, here some help...
Batteries don't develop shorts, they just quit putting out enough voltage to to the job. Smoking jumper cables without cranking the engine points to a major short to ground of one of the wires connected to the battery distribution point on the starter solenoid. Or, as already stated, jumper cables hooked up backwards.
Start the troubleshooting by labeling all the wiring connected to battery distribution point on the starter solenoid. The disconnect them all, and reconnect one at a time and test by hooking up the jumper cables correctly. When you get smoke and sparks, the last wire connected is the source of the problem.
Starter solenoid wiring for 86-91 Mustang
Starter solenoid wiring 92-93 Mustang or earlier Mustang with upgraded high torque mini starter.