Rebuilding a Subaru engine is not something every machine shop can do right. I recently rebuilt a complete EJ25, everything was new besides the rods and crank and it cost me about $750. I did all of the work myself besides the honing and decking.
The alternative that most people take is dropping in an EJ22 out of a junkyard. These can be had for $250 and take a day to do the swap.