I too had a thump at my feet and looked every where for the problem. Found a thread on here about the hood to cowl seal not being as thick as it was when new and causing a thumping sound and you could feel it. Put on a new seal and the thump and feeling in the floor board went away. Drove me crazy trying to find it. Just a thought or something to look at. I found it by having the hood closed and latched and grabbed the hood at the back where it meets the cowl and fender and picked up and it had movement. Good luck and hope you find the cause.
1995 Jeep Wrangler Sahara, 4.0L, 5 spd, 2 1/2 Skyjacker, 1 1/4 Shackles, 4.11 gears, z-plate mod, A/C, ABS, Rubicon Moabs w/ 245/75/16, clutter catcher console, Full Stainless Steel Hinges and Hardware