Answers

It depends.  Your contractor has to get the permiting office's approval and if your space doesn't meet code, he/she must request a variance.  Permiting can take a few hours, days and sometimes weeks...it depends on the local code compliance office in your locale.  An inspection may be done 2-3 times during your project and how fast that happens depends on how many inspectors your locale has.

Are you trying to keep the dog on the deck or off?  How big of dog are you talking about?

Aluminum windows are not energy efficient and they are noisy.  If the window is more than 10 years old, replace it with an energy star rated vinyl window that has bronze outside/white inside.  It will look better, be quieter and the energy savings will pay you back in a very short time.

Do yourself a favor and hire a professional to finish your deck. They know what is needed and will do a good job for you.  Check with your local paint/stain store or building supply center for recommendations of guys that have been around awhile, are licensed/insured and will do a good job.

I would ask to speak with the owner of the business.  If they were responsible for the damage...and you can prove it was them that caused the system to fail (your security company will tell you)...then a smart business owner will want to make it right and reimburse you. If he doesn't, then file a complaint with the BBB, your local Electrical Workers union and if push comes to shove, small claims court to recover damages.