The greatest sentence ever in a proposal is "Any change in scope will affect cost and timing."
Your proposal should always be very specific about what you are doing and what are the deliverables. Research is this many respondants and a report, concept generation will have x number presented to a specific group, CAD will be in this format, etc.
If the client makes a change, it is up to you to lay out the corresponding change in cost and timing. If there is a reduction, you bet your bottom dollar the client will take the discount. If there is an increase, you have every right to add onto your quote. But if the changes are "small" or if it is a long-term client, you have to use your judgement if you want to charge them or not. Either way, it is only to your advantage to clearly communicate their change and what will happen because of the change.
Where it can get ugly is if you omitted something in the proposal that could/should have been in there. That is a judgement call depending on your relationship with the client. I don't think there are any hard and fast rules to apply in that situation.
Bottom line, the more rock-solid the proposal, the less of a pissing match when there is a "change".
For your other questions, you define the end of a phase in your proposal. And I always quoted a phase cost, never an hourly.