Three ways to bill this:
1) Hourly
2) Set price for the project
3) Set price + hourly if it goes beyond the expected pre-arranged time
I'd go with option 3 personally.
The trick is to find the set price. If you go too low, it's not going to be worth your time. You go too high, you run the risk of over-bidding and losing the job.
Try this:
Look at what the average mid-level IT person makes in the NY Metro area (say, $75-80k annual--I have no idea). That comes out to be about $40 per hour. Add 30 percent or so because you are a 1099 consultant and make it $50 per hour. Five hours x 2 days, plus 8 hours on a Saturday = 18 hours. Even it up at 20. 20 x $50 = $1,000
Work up a proposal for the client. Tell them your normal rate is $65 per hour, but you're willing to do it for a flat rate. Give them a 20 hour estimate at $50 per hour for a total cost of $1,000. Throw in an extra 5 hours "free". Anything above 25 hours will cost them $65 per hour. This givesthem some incentive not to "abuse" your time, and it gives you some room in case you run into any unforseen problems (which I will gurantee you will). The client get's a deal, you make some money, and you don't get roped into a 3 week project with those constant as-long-as-you-are-here-will-you-check-out .
Personally, I think 2 weeknight and a Saturday is cutting it close. You might want to bump it up to about 25 hours + 5 "free". Also, as additionaly incentive (I do this frequently) is I raise the price a bit and give them 3 months of "limited tech support" included. Set them up with anti-virus, a firewall, etc. Offer to come in and apply service packs, etc. Make sure this additional work is VERY specific. If they are a small business and don't have much cash, consider doing a monthly bill of 25% or so. Include your "service contract" in this.
