I not sure what your calling a "thump"? Is it something you can hear. or is it something you can feel. Do you feel it in the flight controls, or does it seem to be a "miss" in the engine?.
ENGINE RELATED:
1) Water in fuel. Check fuel system paths and make sure gasculator can trap water, i.e. is it plumbed correctly, in / out. Check the gasculator AFTER the flight and see if there is any water in it. If its plumbed correctly, It should capture most of the water, but some can still get by. I would suspect if this is the culprit, you'll see a lot of water in the gasculator.
2) Valve sticking, usually not one thump, but a series of thumps.
3) Plug fouling, usually a perceivable roughness, unless the other plug isn't firing at all, then its "very" perceivable. ALSO. If you see large balls of lead on the spark plugs, these can become dislodged, and if the timing is absolutely just right, it could lodge between the valve and the seat, keeping the valve from closing for a cycle or two.
4) Long Shot, Carb Ice / intake ice ingestion, Probably not this, as you would probably suffer from engine performance as the ice builds up.
5) Another long shot. FOD, stuff getting through the intake system and fouling the valves.
AIRFRAME RELATED: Something shifting or not secured properly. I would expect these to cause unusual vibrations, but I guess a "thump" could also happen.
1) Look very carefully at the engine mount, and the mount extrusions. Also look at the rubber motor mounts. Is the engine "moving"?
2) Look at the landing gear attach points. Visually inspect these, but ALSO, reach into the Hell Hole and place your finger tips on the attach points and fuselage, Have someone rock the plane front to back and sideways, you'll be able to "feel" the movement.
Also check the wheels/brakes, and of course, the wheel pants. Fly with the wheel pants OFF and see if the problem is still there (Caution, you will notice a significant difference in pitch between "Wheel Pants" and "No Wheel Pants".
3) Same goes for the wing, Put your finger tips across the gap in the leading edge between the wing and strake. Have someone at the wingtip left up, down, forward and back. If you to feel a "difference" between the wing and the strake, then take a closer look at the attach bolts.
Good Luck
Waiter