When I start a new fort it always goes about the same. Long entrance hall which has a raisable bridge by Autumn. The first room that is carved out is the farm in a soil layer, followed by 11x11 rooms with an industry building in the centre. Basically get a masons workshop with 102 stones piled around, craftsdwarf workshop with stone, carpenters workshop with wood, etc. The trade depot room is the same with the surrounding stockpile being for statues which is my primary export.
The reasoning for statues is because I find crafts to get far too much profit per stone and it limits my spending. They are also heavy which means trading can be harder.
I try to put the rooms into grids of 2x2, 4x4, 4x8. This is due to the expansion that happens later in my industry where the rooms become 23x23 with 16 workshops. While I will have stairways leading down I always have 3x3 corridors with ramps connecting each level for mine cart use later.
Typically I'd have 20 statues for trade by Autumn and variably 3 to 6 industry/storage rooms set up. The second year is spent trying to get a squad of dwarfs ready for training, full plate gear with the best metal readily available. I will also spend that year setting up 100 bedrooms, about 10 offices and the hospital. Industry expansion usually happens here too so you can spam items through the manager and keep dwarfs happy.
A fort is never really complete I've found as you will need stone for something, metal for new armour and all that.
So to sum up, end of first year to a functional level. End of second year to hopefully defensible and productive.
I'm not sure what is leading you to having an unplanned layout. But I will try to mark rooms for digging without digging the doorways very early on to ensure my corridors are laid out where I need them to keep the room size I want. Marking the doorways for digging as a room is dug out. I'll also usually only work on one room at time for hauling early on since it can take a month to run 100 stone around with just 7 dwarfs less 2 miners and 2 part time farmers. Most industries aren't needed early on unless you are trying to do something special like cloth, leather, gems, glass and clay. While I dig out a room for them and store the stuff in them, they are usually idle until something is needed. Initial dining room and beds are just put in the corridors until I have time to make dedicated bedrooms and a real dining hall with connected food and booze storage.
Don't know if any of that will be helpful, but hopefully someone's comments will be.