Organization is something awesome, almost priceless. This is the base not matter if you are a single-man-studio or a studio owner.
The problem is most small business, where most freelancers market is, don't want to or can't hire a studio.
If you want to be a freelancer, first learn how much time each task takes. Having a schedule is vital. Also, keep in touch with some partners. If you are better with design, meet a coder. If you are better with coding, meet a designer. If you need someone to write, look up for a just-graduate journalist or a seasoned web writer. Need a lawyer? Meet one.
You will probably need to know:
- a programmer
- a (web)designer
- a (web)writer
- a vector illustrator/photo editing
- a photograph
You can be one of them (maybe two), but for the rest, is better to hire/partner up, as said by Lesè Majesté.
All this was for your Q1.
For Q2:
You need to be sharp when starting a new job. I recommend start with a really damn good quiz to your client. What he want/need? How better this is answered, better will be your time estimative.
Second step is to document this (contract), and make a schedule. If your job takes longer due some reason that regards you or your partners, you should not charge, because it was your mistake.
If you miss the job dead line due a client's request, then this should be charged. Not charged, but documented. A client a two days to deliver wants a lot of features he didn't asked before? New estimative, new contract, new charge. Changing mind is his/her problem (but make sure you offered, or most covered offering those things on first meeting).
Q3:
Charge per job. And sub-jobs.
your designer partner charges $10/hour and will take:
- 4 hours to mockup
- 3 hours to finished skeleton
- 2 hours editing photos
your photographer charges $200 per session (4-8 hours) and will:
- 2 sessions in different days to click client products and store.
your writer charges $30 per '1500' words...
programming usually charges per feature, per hour or per job. What you feel comfortable. But be truly with yourself does not charge per hour if you aren't a seasoned developer. In this case is better charge per job.