my preference on my stove / chimney setup is to have a .04 reading on the manometer max and .02 minimum. up to .06 probably isn't too bad as far as sending heat up the chimney, but you will have to be the judge of that for your installation.
imo that 500* stack temp is very high! 250* on the stack with the stove at 400* would also be a little on the high side for me, especially measured with a magnetic. at 400* i would expect to be in the 175* range with my probe temp. my stack is never higher than 300* and that is with a stove temp above 600*. you will have to take some measurements with the mano and see what your normal temps stove : stack run.
if it is sucking the door closed on your clean out, you better keep the cat on the other side of the room or fluffy might get sucked into the stove!