I think livestock breeding is bugged -- animals born on your land will always be scrawny, and nearly useless for meat. Breeding animals for milk, wool, or eggs should be fine though.
Is part of the challenge that you're going to use wood for all constructions? Or are you fine with quarrying stone to build stone walls and such?
For building upper floors, you can do it from the inside, too, without using outside scaffolding. Ramps or stairs on the outside of buildings will allow goblins (etc) to sneak in through the unfinished upstairs. Here's the right way to do it: Build an up-stair (or up-down stair), and once it's complete you can designate a down-stair (or up-down) on the next level up. Your workers will stand on the lower floor and build the upper one. Once that's done, you can build a floor on the upper level and then walls. To build a roof, build a ramp in place of one of the intended wall tiles, then go up a level and build the roof. Then deconstruct the ramp, and build a wall tile in its place.
Illustrations
build an up-stair on the current top floor
OOOOO
O+++O
O+<+O
O+++O
OOOOO
build a down-stair on the floor above:
+++++
+ +
+ > +
+ +
+++++
build floors on the upper floor:
+++++
+++++
++>++
+++++
+++++
build walls on two sides (don't do the other sides until the corner tiles have been built:
OOOOO
+++++
++>++
+++++
OOOOO
build remaining walls, and a ramp tile (R):
OOOOO
O+++O
O+>+R
O+++O
OOOOO
on the roof, build a floor:
+++++
+++++
++++R
+++++
+++++
then deconstruct the ramp and build a wall tile:
OOOOO
O+++O
O+>+O
O+++O
OOOOO