clifford maxtrix 2.5x, 97 civic, rewire?

I current have a clifford maxtrix 2.5x alarm installed in my 97 civic. I plan on pulling my dash to clean some stuff up behind it. I also wanted to hide the alarm wiring and and move the brain/relays because  best buy  did a messy install.  I know Best Buy advertises a LIFETIME workmenship warranty on there installs. The alarm was installed over 2 years ago. The alarm worked fine and I didn't think nothing of it to check on the installation. I really didn't notice the mess till I did my motor swap a few months ago and I was trying to find an illuminaton wire for my aftermarket gauges.  I know if I took it back to Best Buy they would not take the time to rewire it the way I want.  I am going for a stealthy install.  I am fairly competant about the rewiring. I have done my share of wiring. I am just not that farmiliar with alarms. So would there be any problems if I cut and extended/reroute wires with the battery disconnected for a long period of time? The alarm does have a back up battery installed already.  I was also wanting to add a proximity and tilt sensor.  Will the alarm reset it's self when the battery gets reconnected?  It should just work normally when everything gets reconnected right?  Do I need to reprogram anything afterwords?  And if I do add the other 2 sensors would I have to reprogram it?  Thanks in advance.

You wont have to reset anything.  however it may to harder than you think to clean it up.

I kinda knew that.  Thats why I would rather do it than someone else.  Now how would I add a tilt sensor to the alarm?

Messy meaning wires running across my fuse panel, relays just hanging, the alarm brain tucked behind the carpet and all the wires exposed.  I wanted to add a DEI 507T tilt sensor.  The installer never gave me the orginal wiring diagram for the Matrix 2.5x so I am going off of the Matrix rsx 3.5 that is available on the net, so I don't know if I have an additional or spare ports to hook the additonal sensor.  The only other sensor is a mercury switch on the hood because the installer said he couldn't get a pin switch to work for the hood.  I kind of want to get rid of the mercury switch and try and istall a pin switch under there.  Any help or advice would be greatly appreciated.

Thanks