You're gonna get a lot of replies that vary. Much of what you ask can be found using the search feature on this site.
I want to be able to run a microwave, tv with dvd player, refrigerator (not sure if I want a 12volt or the 110 type), maybe a lap top computer , charge the cell phone/ IPOD, fantastic fan.
All that is possibly with the correct inverter.
Not sure if I will get an air conditioner or heater.
I have a diesel heater and like it. There are many posts on the Espar Airtronic and Suburban propane heaters. Both work well. Portable propane can work as well but electric heaters pull too much unless you're on shore power. Air conditionars are nice but eat up hugh amounts of power and are suited more for shore power. Danhard is SMB's choice unless it's a roof top style. An on board generator is another way to run one. But I have the old Starcool and it works great on the road. On AC power it might knock off 15 degrees of the outside temp. 100 out, maybe 85 inside...not much for the cost. On the road it will freeze me out.
I would like to add maybe 4 or 5 12 volt outlets and 4 or 5 110 outlets.
Sure why not.
I am not sure if I should get one or two batteries. Maybe buy 1 now and add 1 later?
What batteries do you recommend? Brand? Model number?
I suggest a good 4-D AGM such as Lifeline or Deka. I'd stay away from wet cell batteries but thats just me.
What type of separator should I get? Brand? Model number?
I got rid of my surepower 1315 and went with Blue Sea 7622...I like it.
What type of inverter should I get? Brand? Model number?
I have a 2000w Xantrex prosine. It's also the main charger.
What type of battery charger? Brand? Model number?
My inverter does the charging but don't forget solar.
Will add an outlet for shore power. Model number?
Most RV shops have them. Mine is 120v 30 amp model
The seperator charges the battery while driving?
It disconnects when needed and charges whenever it see a charge voltage.
What associated hardware, cables, fuses etc. do i need?
I'd run 1/0 copper between the batteries and 4/0 or 250mcm to the inverter. Might be a good idea to fuse it with some 300 a fuses but most are not. Install a GFI for stuff by the sink area.
Those are just a basic answers. This link might help and has other better links within it.
I'm sure others will chime in with good info as well