Thermostat problem?
Did you use the recommended Ford/International Thermostat? Apparently some of the non OEM thermostats you can buy can give you trouble on the 6.9l motors.
Did you check the air bleed ball next to the Thermostat under the thermostat housing for free movement. If your coolant was bad than the air bleed ball could easily have fouled up too and not let any air/vapour bleed from the motor to the radiator. If the hot coolant does not reach the new thermostat due to a vapour pocket behind it it may not open.
Fouled-up is not the word. That little ball bearing was impacted in the thermostat tube with hard crud that I had to pry out w/ sharp screwdriver. I used a Motorcraft thermo from the dealership and did the prestone flush when I flushed the system in the first place. I appreciate the advice I could have missed the air bleed if I didn't know to look for it.
If you want to you can and should remove the block drain plugs one each side of the block and put some twist open drains from the Help section at the A/P store. You will then remove 99% of the old/block coolant. Only use std old green A/F and distilled water with the the DCA 4 or VC 8 sca's........Napa cool?
CAUTION:
The specified/required thermostat does not contain an internal bypass, since the bypass is located in the cylinder block. Whenever the thermostat is replaced, it is mandatory that only Motorcraft E5TZ-8575-C or Navistar 1807974C94 thermostat be installed.
CAUTION:
Do not attempt to repair any thermostat. It should be replaced if it is not operating properly.
Check the new thermostat before installing it for correct opening temperature. Before suspending in boiling water, with a flashlight check where the rubber and the flat metal flange meet for bad seal. Tstat should start to opening barely at 180-192f, fully open 200-212f, allow to cool and check for rubber seal again.
Removal: Disconnect batteries, drain 4+ gals A/F, remove: as required, fan belt, alternator set aside, alt bracket, remove filter support from fuel filter then e/block. Disconnect upper rad hose at rad, remove tstat bolts and housing. Clean both faces, depression and holes in block, ensure check ball in goosekneck is clean, free and rattles "do not remove".
Installation is reverse proceedure, I do not use sealant on gaskets and faces. REMEMBER the tstat pellet(copper end) goes into the block. I do use a "very small amount" of sealant on the edge of the tstat face when installing into the recess, now go for coffee, allow sealant to setup, this has saved me from tstat slippage when the gasket and goosekneck are installed. Replace all items in reverse order......
Manifold bolt torque......... 20ftlbs




