I would definitely use your tax software to get an idea of estimates.
Likewise, for Federal, if you pay in 100% of your 2007 taxes (Look at line 63 of the 1040 - Total Tax - though you can deduct any credits (child tax credit?) to figure your true tax for the year)... If you pay in 100% of that for 2008, with your withholding, then you do not have to pay in any estimates for the year. This is called the "safe harbor" rule. Generally helps people avoid IRS penalties if their income is unpredictable, etc. States generally follow the same rule. You can wait until next April 15th to pay it in, when you do your 2008 taxes.
Anyway, 35% seems fair since clearly much of it will be taxed at the 15% Federal rate, and some at the 25% rate. Plus 15% self-employment taxes. If you have the discipline to set it aside and not touch it? I wouldn't bother doing any estimates. Then you can get an idea by your tax situation when you do your 2008 taxes, and you can do the 100% rule the following year as well. (Which means you would probably start paying estimates in 2009, based on your 2008 tax).
I am not sure what state you are in, but same kind of thing. Don't forget the state.
I agree on the ROTH advice. The general advice I have for SEPs is to figure it out when you do your taxes. Who knows, you may have extra money early next year and decide to fund a SEP to lower your taxes. But trying to figure it out before the year end is usually nearly impossible. So when you do your taxes next year, see how much you can put in your SEP, and decide if you want to put in any over your ROTH.
But yes, definitely fund the ROTH first.
& here is a good article on the subject:
How_to_avoid_underwithholding_and_its_penalties: Personal Finance News from Yahoo! Finance
Just to clarify if anything I Said was confusing...