Re: 01 V6 brake issues..
Did you use a repair manual (Haynes/Chilton) when doing the job? Perhaps you missed something, or a step. I first thought that all vehicles' brakes were generally the same but began to notice differences. My Dodge's rear drums are simple enough. I would rule out the 'thump' being brake related unless you're positive the shoe isn't dragging and has been installed properly. One thing I would check for is a bad wheel bearing (easy to do yourself; jack up the wheel in question, place one hand under and the other on top of the tire and rock the tire/wheel towards your chest. If there is play and the wheel rocks, your bearing is shot). Are you using the right lube on the spring and around the cylinderto prevent noise/rust?
It's also possible the brake shoe might be dragging or your brake proportioning valve isn't sending the correct pressure to the required wheel.
Check the emergency brake and make sure it is disengaging all the way. Also, when was the last time you changed the rear axle gear oil? It'd be wise to visually inspect the pinion and ring gears for any wear that might be causing a thump sound.
With any luck you'll get this problem resolved. I can't say I've ever had brake issues like you mentioned, but I know I wouldn't be happy!!!!
'11 Ram Quad Cab 4x4 SXT 5.7L HEMI (stock); 48,500m
'06 Pontiac G6 GT 3.5L 220hp; 64,000m
'12 Chrysler 200 Limited 3.6L 283hp; 28,000m
'99 Taurus 3.0L 2V Vulcan 145hp; 154,300m - Traded
Amsoil in all vehicles!