97 Explorer Sport alarm bypass

I have a Ford Explorer Sport, 2wd, V6, 4.0. Had to replace the alternator. Now the only way to start the truck is to push the bypass button located under the steering counsel by the driver door. On top of that, when I open the door, the lights inside and out start blinking on and off, like there's an alarm going off. I was told to pull the fuse and it would stop. No such luck. Only way to get it to stop and start the vehicle is to push the little black button. If that wasn't enough, the battery gauge is barely registering when the truck is running, and its a new battery. Alternator and battery have been checked twice and nothing's wrong. It seems to me, and I've heard the same from a couple different mechanics as well as 4 auto parts stores, that there's a major short in the "alarm". But even after going thru all the joy of doing everything that I was told to do, I'm still having issues. Any body have a clue or suggestions to what the problem could be?

So all these problems started after replacing the alternator?

Since you mention a bypass or valet switch under the dash, it sounds like you have an aftermarket alarm installed. You'll need to locate the aftermarket alarm module and unplug, then see if that has an impact. The alarm though should be separately fused though and would not be able to draw enough current that the alternator couldn't support it so it sounds like you have other issues as well. Have you installed a series current meter with the positive cable to see if there is a significant draw on the battery when the engine is off?

-Rod