I have the 4.6 DOHC in my 96 and after replacing the plugs and coils find that cylinders 1 and 3 are both bad. My engine only has 80k on it and I really don't want to replace it with other engines out there with more miles. I know it will probably be the best to pull the engine completely out and work on a stand. I am curious to know what kind of job I am looking at to replace my cylinders? Is this going to be worth my time in the long run?
Well that sounds like rebuild time. Your options are buy a short block from any # of places on the net that have 4.6 shortblocks
Build it your self will probably by close to 2K when you figure in new Pistons and rings,bearings,gaskets and all new bolts because OEM bolts are TTY (one time use). I'm sure you can do it cheaper than $2K but you really have to shop around for good prices
Budget, goals? If you just want to get back to stock performance, you should be able to find a complete motor for your car for $800-900 in excellent condition. If you can't find a '96-98 motor, then a 2001-2011 2v 4.6L Romeo (01-04 Mustang or 01-11 Crown Vic/Marquis/TownCar) can be found with low mileage and nearly as cheap (cheaper if you look for a Vic motor).