Coolant and tranny fluid flush?

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For the trans fluid:

Drain the trans. Then pull the shifter off and refill from the top. As for the fluid. I've been very happy using Mobil1 ATF. I plan on switching to Royal Purple Synchromax soon. So I'd suggest either one of those.

For the coolant:

Drain the system. Pull out the thermostat then put the housing back on without the thermostat in it. Disconnect the radiator hoses from the radiator. Shove a garden hose into the top rad. hoase and turn on the water full blast. All kinds of **** will probably come out the bottom hose. Just let it run for a while.

Then run the hose through the radiator to flush it.

Clean out the overflow tank as best you can.

Put a new thermostat in. Reconnect the radiator hoses. Fill with coolant and burp the system.
 
+1 on Mobil1 ATF, I had really good luck just using the hand pump that screws onto the fluid bottle and going through the screw in plug, got it from advanced auto real cheap, It beats having to replace the shifter seal. I heard that ford revised fluid amount for the 3650 to 3.55..... thats what i did and feels great.
 
With a lifted car, the trans fluid swap is as easy as they get. Drain and fill. As 03machone posted, buy a gear oil pump for < $10 from an auto shop. It screws onto the bottle and pump the fuild in the fill hole.

I used Amsoil ATF and it immediately shifted smoother. I'm sure M1 would do the same.
 
Any reason you are draining the fuild on a manual trans at some odd 50,000 miles ? You really don't need to change that fluid all that often unless you have been cooking the hell out of it or it has problems shifting. If it has problems shifting there are often other issues however. If you are planning on driving it like you stole it then a different trans fluid might be in order but if you are just daily driving it, it is likely a waste of time.

I ran my stock 3650 well over 100,000 miles and never touched the oil in it until I pulled my factory clutch out and put a T56 magnum in....