Copying table into docx makes page numbering go haywire

It sounds like you also snagged a section break. And it sounds like this must be a big table. I suggest using Excel as an intermediate step. You won't be bringing any Word formatting along for the ride.

In your table file, turn on hidden characters (the paragraph mark) - easier if you just hold CTRL+SHFT+8 (basically, CTRL+*). Now, click anywhere in the table. You'll see a small square icon in the upper left corner. Click on it to select only the table. CTRL+C to copy the table.

In a blank worksheet in Excel, right click in cell A:1. In the Paste options, choose the 2nd one - Use destination formatting. Now select the cells containing your table and CTRL+C to copy.

Now your thesis doc... make a couple of copies before you proceed. Then, do the CTRL+SHFT+8 again to see the hidden characters. Move the cursor where you want to insert the table. Right click and choose Use destination formatting again. It won't be pretty but it will be easy enough to make it look good.

You might check your page numbering before you spend time jazzing it up... 

Click anywhere in that blah table and click the square icon appearing above the upper left corner (this selects the entire table. Now go to the Table Design ribbon and choose something classy for your thesis. Notice styling headings, banded rows, etc. are to the left.

If it's still wonky, reach out to me in Linked In, Matthew. I'm in the process of revising 30+ SOPs and would love a distraction.