If you're going to use an old case, make sure the airflow is sufficient. I mean, boxes of today are ready for, or even preassembled with, 120mm fans or larger at both ends whereas a vintage solid steel case from the late '90's might have one 80mm hole in the front and one 60mm in the rear, both of which had more steel than hole in the grille.
Back to your question: Yes, just take all the guts out and start all over. Cases have had standard places for motherboard screw holes since I don't know when. Just make sure you have the brass raiser bolts only under the mobo holes to prevent shortcuts.
Some hints concerning classifieds, or any other place for second hand stuff: Start with a motherboard. A mobo sold with a CPU (processor) it's been used with should be fool proof compatible. Many times people change RAM (memory) at the same time, so that might be included, too. Those three components have the most variables concerning compatibility issues. After you've got them, the rest is mostly a question about performance issues.
Remember, you can also act as a customer on the classifieds board. I mean, like putting a request:"I'd like to buy a decent rig for playing AH better than with my laptop. Partial delivery accepted, advice appreciated."
*Ask before you buy anything!*