$3k sounds high to me but its best to look at the "Scope of Work". If it indeed only includes running small gauge wire to some windows and doors, its a rip, IMO. For $3k you should be able to get a hearty panel, can, wiring, boxes, sensors, contacts, etc for that amount of money, turn key.
If you just want the prewire and not use ADT or Brinks but still pay their monthy fee it could be:
24 x $26 = $624
36 x $29 = $1,044
Or somewhere inbetween, maybe higher. AND you may not get the prewire you want. It is ill advised to let ADT, Brinks or anyone else just put in whatever THEY think you need. You MUST have a plan and get EXACTLY what you want in your prewire. You should be able to find just prewire to windows, doors and a few sensors for that amount. no equipment.
Is this a custom home or a big builder? If its a custom, most likely your builder will bend over backwards to accomodate, or should! If its a tract builder, they may be a bid more limited and not as resourceful (you can always deal with someone OTHER than your project manager/supervisor, go over their head if they are buttheads). Remember, ADT/Brinks likely sub out all their prewire/install work to local clowns that make $8 to $10 who hour and have had little if any training. Playing with fire there my friend if you want to eventually use their prewire for anything other than the junk they install, and trust us, they will install exactly that: JUNK.
There really is not much to running security wires. You really should consider another source to run some wires for you instead of what I consider failing on two sides: 1-ADT or brinkman prewire (limited, may not be what you want, could be wireless, not enough) and 2- Locked into the THAT service provider (overpriced, poor equipment).
Get your plans, draw exactly what you want and where, label what wire, what contacts and then shop around. I cant imagine not finding a prewire company that can blow $3k out of the water