Ok I have a 98 ford escort 4 door sohc, Well I recently had the transmission replaced and after it was replaced the main seal keeps leaking,, for no reason. Themechanic has pulled it twice and can't figure it out. After it runs for about 45 min it starts to leak,where the transmission meets the engine where the main seal is. Please help.

Hummmm, very tough call to make here. Oil leaks can creap up in weird ways. Let me guess... When the 'new' transmission was installed, there should be dowels on the bellhousing that line up with the engine so everything lines up nice and neat and bolts together tight. So no matter what torque or load you put on it, everything stays in line.
Did the tech go to Ford and try a OEM part? I bettin' he did. And hoping no spacers are left off behind the flex plate.
You could possibly have a thrust problem with your engine bearings, or just a worn mating surface where the rear main seal seats.
Best thing to do at this point is try getting a product that 'swells' the seals and claims to stop oil leaks. Never tried it myself, but heard it works occasionally.