I'll try to go through your list, seeing as I'm the first to answer.
Only stash items in a settlement container of a settlement you manage (a container inside the green boundary in other words) - all other containers will empty and respawn after a few ingame days.
Stashing items inside a workbench is the best way to store junk items for breaking down into materials later, so do that in a settlement workbench of the settlement you want to build up. Connecting settlements with trade routes also joins the materials stash to that connected settlement. You can then build things using the junk automatically.
1. Only pre-made locations as you need a spot with a workbench, which you can't legitimately build from scratch, though I have just found a console command to build a workbench, if you're on the PC. Scroll down http://fallout.wikia.com/wiki/Fallout_4_console_commands to find it - you can then build settlements anywhere (haven't tested this myself yet though).
2. Can't flatten the ground itself, but use the concrete foundations with wood floors (found under Wooden Structures - Floors) to make a flat base to build on.
3. Best way is to assign people yourself to crops. Otherwise you can see if a crop has someone assigned by looking at it when in workshop mode, it will have a green people icon instead of red.
4. Scavengers and the scavenger workbench means you get extra mats to use to build stuff in the settlements (and for mods and so on). They're awesome, you'll need to manually assign someone to that workbench though.
If you're on the PC a good mod to use to keep track of assigned settlers is this - http://www.nexusmods.com/fallout4/mods/2017/?. If you really get into this settlement stuff I know a few other fun mods to use as well.