Here is what I would do if I had just bought a used sn 5.0...and I would note it does not assume an engine replacement or tranny replacement...
Disconnect the battery to start. This will avoid you frying electrical stuff and also reset the computer. Which will help with the last step I am going to recommend you to do.
I agree with the tune up items. Don't forget the fuel filter. People tend to skip it because it is slightly more difficult to do, but you really need to change it so you know it is good.
Now I don't know your particular level of knowledge. Perhaps when someone says "clean the MAF" they may as well be speaking in Chinese...but, maybe you know exactly what that is...
So, at risk of sounding like I think you are an idiot...which I do not...but just so you know...
The MAF / mass air flow sensor is in the air intake tube that runs from your passenger side fender to your throttle body / upper intake. When you change the air filter, you cannot miss seeing it. It should have a sticker on it, but that may have gone away as a function of time. In any event, there is a wiring harness that runs to it. It is in a big black plastic housing. Go to my profile and look at the pics of my engine bay and you can clearly identify its location. Anyhow...
Remove the MAF from the housing using a T20 Security Torx bit. You will notice that the torx screws that hold it together have a little nipple in the head. The security bit has a little hole for the nipple to fit into.
Use NON-CHLORINATED cleaner to clean the white wires after you get it apart. They make MAF cleaner, which I THINK seems to work better, but I may be fooling myself. As long as the cleaner is NON-CHLORINATED, you should be fine.
Now, some people will rub the wires a bit with a Q-tip to help clean them. Personally, I don't touch them. They can be fragile and if you damage them you will be buying a new MAF...
Anyhow, spray the MAF, let it dry, put it all back together. Now, you have a tuned-up car. Maintenance issues should no longer exist, right? When its all back together, and assuming it took more than 20 minutes or so to do all the tune-up stuff, you will have cleared the computer by having it disconnected. No codes.
Hook the battery back up and take the car for a drive. Get it to temp. Drive in town. Drive it at highway speeds. Whatever. Just give it a drive to let the computer "learn" again...
Does the CEL pop up? Even if it does not, after driving it for a while, I would scan it. You want to see if there are any issues being reported after you have done all of the maintenance parts.
Well, StangNet won't let me post a direct link to my preferred site...and there is nothing in the '94-'95 tech sticky related to pulling KOER codes...
Google "SBF DIY KOER" to find the thread from another site that has an sn95 5.0 specific write up with pics on pulling codes.
Or, use this site, which has not nearly as nice of pics...
http://www.troublecodes.net/Ford/
Or, buy an OBD-I scanner:
Amazon.com: Equus 3145 Ford Digital Code Reader: Automotive
Anyhow, let us know if you have issues after getting the maintenance stuff done.