First off when I started to build my first AR I knew that I intended to build many more so I bought all my own tools (mostly all replaced by better quality tools). I have built over 115 from scratch and done depot level work on several hundred more. First welcome to the fold (read... addiction) of building custom AR-15s. Second these are my opinions crafted over many years of working with these incredibly functional and versatile weapons system nothing more.
To answer your questions:
1) Stainless vs chrome-moly (Actually a steel alloy including chromium & molybdenum)
Stainless is more a visual and maintenance thing that anything else. If a chrome-moly barrel is properly maintained (oiled and cleaned) then there will not be any noticeable difference in longevity or performance. Don't forget though that stainless can also corrode and rust if neglected I have picture if you would like to see.
2) For a 16 " carbine barrel a 9" rail will cover all but the longest gas blocks.
3) One way or the other this will came down to having the tools, I'm not trying to avoid answering the question but the cost of the tools may direct your choice. In light of this you might want to get a low cost upper built to you specs (PM for links)
This is not intended as comprehensive list but just the basics:
AR-15 Armorer's Wrench
Upper receiver clamshell, Action block, or Geissle reaction rod
Torque wrench
Forward assist Roll Pin punch
White lithium grease
Good kit to get you going
BROWNELLS - AR-15/M16 CRITICAL TOOLS KIT