Some of my thoughts since nobody else has posted.
Pulling up on the handle will not set a car alarm off unless the handle is connected to the interior lighting system, which the 98+ Contours are not. (I'm not sure about pre98s.)
Easy way to disable the trunk release cable is to flip the orange switch that is located in the trunk by the latch. You may want to do this regardless of alarm, since your Cardomain states you have a sub.
I had an alarm that went off with every little noise and I will tell you it is more annoying than worth it. You can't park the car on the street, since even the quietest car driving by will set it off. You can't even park near the street, since booming stereos and loud exhausts will set it off.
The good thing is that most aftermarket alarms have a variable setting so you can set the sensitivity. (Mine did but I never changed it)
If you're this paranoid, your best bet is a paging alarm system. Not only does the paging remote control offer an incredible range, but it's very convenient to know if it is your car whose alarm is going off. It might be out of your price range. I got mine through shady means (using friend's BB discount) but I think they run ~$350 installed. Unless you REALLY know what you're doing, getting it installed is the best idea. The only disadvantage is that the remote eats batteries, I replaced mine once every 1.5 months. But it was AAA battery so it was cheap to just by an 8-pack.
As for relocating the battery, it's not really worth it especially if you get a paging alarm. My alarm had a mercury switch installed in the hood so lifting the hood set it off. By the time they lift the hood, locate the battery and cut the wires, a few seconds have passed and your remote will have beeped at least once.
, and have been very happy with it. They do lack in the instruction department, so if you plan on doing it your self, take your time and DO YOUR HOMEWORK!! Wouldn't want you to fry something!