The short answer
Plan for the complete project, not just the home. The largest additional costs usually come from land and homesite work.
Common cost categories
Your project may include land, surveys, clearing, grading, foundation work, delivery, installation, permits, utility connections, septic or sewer work, steps, skirting, HVAC work, inspections, taxes, insurance, and closing costs. Which items apply depends on the property and written sales agreement.
Build one list with a responsible person for each item
For each applicable cost, record the provider, written quote, what is included, and when payment is due. Mark missing estimates as unknown instead of treating them as zero.
Check for overlap as well as omissions. For example, do not count an installation item twice if it is already included in the retailer’s package and a separate contractor’s estimate. Update the complete budget whenever the home options or site-work scope change.