My 2000 forester with a 2.5 engine and std.transmission has a rod knock and blown head gaskets 273,000 miles ,I just purchased a 2000 forester with a good running 2.5 engine ,the car was hit in the back and totaled,this car has a automatic transmission ,I've pulled the engine and plan on doing head gaskets and timing belt ,installing the fly wheel ,my question is,what needs to be done to the engine because it came from a automatic and going into the standard?

It should be plug and play. if in doubt, use the intake form the original engine. Do the baffle seal behind the flywheel.

nothing really.  remove flexplate and install flywheel.

 

main concern is the EGR situation of both engines.

 

get a timing belt kit from rockauto or amazon for $120-$130 - all new belt, pulleys, and tensioner.  don't leave the 15 year old tensioner in there.

yeah, just unbolt the flex plate and put the flywheel from your car on there. Every other part should be identical. You can make a bit of $$$ back parting out the bad motor. Did that with a legacy a few years ago. The bad motor paid for the replacement motor by the time I sold off the good heads, intake, sensors etc. Plus a hefty block is worth about $10. in scrap.