1999 Mercury Marquis mud?

i flushed the cooling system about 10,000 ago it looked like it had mud in the overflow. it took 4 time to get it all out. now its over heating again and l took it to a shop. i told them when it had been flushed and that it had a new thermistat in it. the told me it was the intake manafold had a leak and that it needed replaced. $1,522.00 i said no thanks ill take care of it. i got the parts and replaced it. and yes the old one was bad. but it would still over heat. so got new water pump and instilled it. and still the samething. >.< i pulled out the thermistat and ran it that way last week. no over heating :) but the mud came back? it looks like mud and is sandy looking. can you help be plz. also what way does the theremistat need to be instilled on this car its the 4.6L. the book didnt say and the pic had the long side down. that is the way i installed it. i didnt check it when i took it off.
thanks for your help
Brian