Engine Fix Or Swap?

Hi All, got a 2003 Mustang GT Convertible in winter storage. I bought this new in 03 and drove for many years. It blew a plug and needed a head replacement and I did a bit of work to it to replace head. It has been sitting and I want to start to think about getting it up and running again. I plan some minor restoration/customization. It is pretty rust free and was always a good daily driver. Engine has about 180K miles. For this post I have 2 questions. First, to get it running with the new head, I have been trying to get the driver side timing chain and cam correct. The passenger side chain was never removed. I marked both chains and sprockets before removing, but the driver side valves do not seem to be in the correct position while rotating the engine manually. I was hoping to just pop the driver side chain back on in the marked positions to restore the timing to where it was. Any insight on this?
So for part 2, question is should I even bother with trying to get the existing engine working due to its age. Is this a good time to start thinking about dropping a crate or remanufactured engine into the car. The budget will not be too great, but given the amount of mileage on the existing motor, I'm wondering if it is time for a swap. So I am looking for recommendations as to what a good swap would be. It would have to involve some compatibility with the existing 5 speed manual transmission and ECU/computer. Although I would entertain more traditional normally aspirated and fueled solution or any power adders. Not sure if there are any concerns about keeping the correct engine for numbers matching car in long term. Will probably hang to to the existing motor to play with outside of the car in any event.

Thoughts, recommendations, etc?

Revisiting this thread. Wow has it been that long. Anyhow, I got side tracked with a Gen 2 Ford Explorer project and finally have the 03 Mustang back in my garage. as mentioned, had a problem with original head, replaced it and thought I marked timing correctly, but the engine seems to interfer when test rotation.

I will likely be pulling engine and replacing as teh car will need to be torn down a bit for clutch, suspension replacement and some general body mods. More on that in another thread. I am willing to take another stab at getting timing right, but will need some guidance.

Ultimately I am looking for suggestions on replaqcing the motor with a rebuilt or other motor. Does another 4.6L X code motor fit the bill. Longer trem I was thinking anout power adders (supercharging) and may require moremodifications to stock.

In any event, can I get some ideas on what to replace this with?