Doc here,

imp:
First, I hope you mean 100 AMP Alternator..not WATT..
Not knowing what type of Audio System you have, (how much power is consumed, and how it is used, like sitting parked or driving) It's Hard to say if it is the source of drain or not. And the location and cable size is another factor.
Be sure the Alternator belt is tight.
Inspect and clean the cables for Corrosion, and be sure they are tight.
If the starter is not engaging when this happens (no clicks or noises) Check the neutral safety Switch for in-op or out of adjustment conditions. You can bypass it for testing. You can also try the "S" terminal to the battery cable bolt side of the solenoid with a screwdriver to see if it will crank, this all points to the NSS as a problem.
Start the Car, and let it warm up about 5 minutes or so, at warm idle, get your DVOM out and set it for V X 50 or autorange. Measure across the battery, it should read 13.95 to 14.4 Volts at idle, no load conditions. If not, you have an Alternator or regulator problem. Is this externally or internally regulated? (Not a Ford guy at all!) ..
Have the Battery Load Tested at the local Auto Zombie, for free, If it has a Bad cell it will fall off rather quickly, indicating your battery needs replacement..
Remember: EVEN new parts fail, a lot of times right out of the box! Do the testing FIRST..don't throw parts at it before, you probably won't fix it and it gets costly!
If your system is High Wattage amp and deck (like 1500 watts or so) You should upgrade your cables to 0/0 or 0/1, to avoid heat loss (and current drop) To the battery, as well as the cables to the amp (especially if located in the trunk.)
Check all your grounds. You should have one cable to ground AT or near the starter, to any handy bolt, from that same bolt, run another 0/0 to the frame. Also from that same bolt run a 10 gauge wire to the firewall and ground it. Also run another to the alternator Ground lug, and /or mount bolt. Everywhere you ground a wire, Clean, and Burnish off paint and dirt or grease from the area, and add a star and lock washer.
The starter motor could have a flat spot, but If , when this occurs, you can start it by jumping the "S" to the battery cable bolt, that will rule that out.
As far as bypassing the computer for start up only, I doubt that is a possibility, as it is all or nothing at all if it is injected , and has sensors that dictate haw the engine fires..I'd leave it alone anyway, If it is a road driver and your state has smog regs..it could leave you walking on your next biannual!
Doc

imp: