It seems that the plug I've used for the radiator hole had fallen down during the flushing letting air in the system. I don't quite know when it fell down and how much air there is in the system but I don't remember removing it after I'm finished and I don't know why I did not pay any attention to it at that time. I'm trying to find a way to let it out and compansate the amount of air with additional oil. I used 10 qts of oil while flushing and I got ~10qts back, so the amount of air should not be much. To get the air out of the system, I run the engine with the tranny fluid check dipstick off, I put the transmission lever in all positions for a couple of times for at least five seconds. I let the engine run a bit more and check the fluid level and add no more than 0.1 quart of fluid. Then I continue to run the engine and play with the shift lever, let the engine stop for some time to let things drain down for 10-15 minutes and start over again. I believe this is working, however, I'm not sure how effectivelly. The next idea I have is to completely reflush the transmission but with at least 20 quarts of fluid this time to make sure that there's no excess air in the system. Other than these I'm totaly open to any recommendations and highly appreciate any help. Thanks in advance.
Ihsan

Perhaps the car was on a slight incline which had it resting against the transmission stops. Or the car had been jacked up or on a ramp for either the end links, tranny flush, or both. This would cause the clunking you describe.

I flushed my tranny and certainly never experienced any such "banging".

I'd say it is not normal at all.

however, as long as it's now shifting OK and the fluid level is good then all is probably OK.

Dunno much about tranny, but perhaps there was some kind of air pocket in the hydraulics that worked itself out.

Good Luck with it !

Not sure. Did you check level when hot and running afterwards? Mine worked perfect. I also added BG transmission conditioner. About $17 a can.