Many journals will waive page charges if this presents a financial hardship for the author; color plate charges are less-readily waived and would at least require evidence that the color is essential to the presentation of the data e.
Of course, any changes should be done with caution and tact. In this way, you will be able to see if any of the stages takes too long, and you should pick up your step doing it. Generally speaking, academic papers follow more or less the same conventions.
Revise the manuscript. Enjoy the moment! This step involves three major tasks, each to be carried out in the order given: Make major alterations: Fill in gaps, correct flaws in logic, restructure the document to present the material in the most logical order.
Your thesis statement could change as you gather more information; however, coming up with one early keeps you moving in the right direction.