"I went to the gross margin report and it shows estimate cost* of 6254.64..."

The "estimated cost" shown in the Gross Margin report shows the estimated cost before markups. It does this because gross margin is the difference between your cost and what you collected for the job. The gross margin report assumes you will collect whatever you have invoiced so far.

"...so I went into print purchases and it says $3031.15 as the costs. "

The costs shown in the Purchase Listing report shows only the cost of the materials or subcontracts that you have entered for the job - before markup, and it does not include labor. You can see the labor costs (before markup) for the job by going to Reports > Job Transaction Reports > Labor Hours. The sum of purchases ($3031.15) plus labor costs ($1828.75) is the total of your job costs - before markup.

"I then went into costs to complete and it says 4859.90."

The "Actual Cost To Date" column in the "Cost To Complete" report shows the sum of your purchases and labor costs - before markup - for the job to date. The number shown is correct: $3031.15 + $1428.75 = $4859.90.

"I then went into estimate vs. actual and it was 4270.72."

I'm going to guess that you ran the Estimated vs. Actual report with the "Include Incomplete Items" box un-checked. If you check that box and run the report again the total actual costs will come to $4859.90.