Bly,
I have tested almost all the fighters at a minimum of 3 altitudes (1, 10, 20k) and have found all of them to be within 2 mph or so (at whichever version they were tested). One of the things to remember is it takes these planes a very long time to hit the max speed... sometimes 5 minutes or more.
If you really want to test them, here's a way...
Go to a few k above the altitude you want to test. Dive down to your test altitude so you are going faster than the published speed. Let your plane slow down (at full throttle) until its speed is steady (again, this may take a long time). Once it is steady, reduce throttle and let it drop a couple MPH, then apply full throttle and let it climb back up. When you can match the speeds, you have found the true top end.
Edit: Make sure you are using True Air Speed on the E6B