Ok, here's what I finally got to doing:
All pictures were with center point focus only, evaluative metering, using tripod, MLU, 2 second timer, refocused between each shot...no shake evident, 5 shots for each setting, posted at picasaweb.google.com/ztross under Brick Test Shots
At the 200mm end of my 70-200 f/4L
1. with a TC, filter at f/5.6, 25'
2. with TC, filter, f/8, 25'
3. with TC, no filter, f/5.6, 25'
4. with TC, no filter, f/8, 25'
5. no TC, filter, f/4, 25'
6. no TC, no filter, f/4, 25'
7-12. Repeat 1-6 but at 75-100'
At 25' were all pretty good. Without the TC the shots were noticeably sharper even wide open. At f/8, the shots are noticeably sharper than f/5.6 with the TC. Filter didn't appear to make a difference here.
At 100', the filter still didn't appear to make a differnce, or at least not much of one, and the weird thing was, it appeared to slow down my shutter speed by about 20%. I had been getting Tv's of 1/800 with a filter and 1/1000 without at f/4. Same thing happened at differnt Av's and with or without the TC attached...interesting...
Anyways, at f/5.6 vs f/8, obviously stopping down helped. The filter didn't seem to affect the focal plane. I am planning on heading out while there's still light and trying from further away. At f/4 (no TC) vs with TC, it's still sharper wide open.
My conclusions: filter has little to no affect at close distances. I usually shoot outdoors soccer/frisbee games with the TC on (anywhere between 25' and 300' plus, so I am going to need to get further away and see if that affects anything. TC degrades image (duh!) but by stopping down 1 stop it helps A LOT! That's all I can say for now.