One thing I don't think I've seen throughout this thread but is common on almost any job: change orders.
Regardless of whether you've quoted, bid, or negotiated a custom deal on a job, you should always have a section which deals with change orders. The changes requested after the 'final' design and contract are in place, even on government jobs where profit caps are in place, is often the most highly profitable part of the total job.
I'd say 1.5 x your regular rate for construction phase changes is a reasonable start. Having a good 'change control' process:
1) documenting any request (date it was requested, by whom, scope of change noting what was originally designed, etc.);
2) quote for cost of change
3) schedule of change. Even if it doesn't change your schedule, include a comment stating that it won't impact the schedule. Be careful though, if you're taking time out to do doc prep, design modifications, or such, you could be impacting your schedule. Many, many contractors avoid liquidated damages based on the change orders impacting the schedule and it's perfectly legitimate.
3) Submit the change request you've documented, the cost quote and the modified schedule to the person or office that has the authority to authorize the change. Do not do any work until it's signed and added officially to your scope of work or you could be giving the additional T&M away.
This is valid for small jobs as well as large jobs and even if you 'give' the additional work away as a favor or to garner repeat business or referrals, it's might be a good idea to document that change and document it as an "n/c" item, either in your own file or with the customer's statement.
You might end up being surprised at how much you're giving away if you begin to track the changes which occur.
