yeah, definitely avoid aftermarket alarms... they usually butcher your wiring with tons of cuts/splices/scotchloks/extra relays/modules.... all of which will cause problems eventually.
factory wiring that's unmolested should last near forever, as long as the insulation doesn't rot off from heat in the engine bay, or some squirrels don't have their way with it.
as soon as you start cutting stuff without properly soldering/shrinktubeing it tight you will have corrosion issues from humidity or weather.
i could probably still count the amount of alarms i have seen removed on both my hands, but that's still quite a few, usually because of issues you are describing. some of them just wouldn't plain start also, or would if you figured some way of coaxing it by wiggling modules or battery disconnect. the fun ones would have random shutdowns while driving or erratic alarms.
anyway, if the car doesn't have a factory alarm, then leave it that way
and i would advise you start removing your dash panels, and stuff, tracking down all the alarm hardware and removing it. then start matching up wire colors/gauge where they used to be, solder it all back together and seal it with shrinktube.
and as for you OBD connector, i cant imagine why the heck they would have touched the wiring for that either... but maybe if you repaired it with something even temporarily you might get a scan out of it. otherwise if the connectors damaged go get another one from the salvage yard out of any number of cars. make sure it has a couple inches of wire sticking out of each pin, then get out the solder and make it right. you can always tuck the extra wire up under the dash.
oh, and if you dont like solder you could always use some weathertight crimp connectors. they work fine, i install a lot of radios and stuff with em, and that's what i used on my intake swap for the wire extensions. couldn't find my old soldering pencil, and its not that great of quality anyway...