Well...
My '87 LX N/A has just a tad over 204,000 miles on it.
Since I bought the Mustang secondhand (as most of us here did) and didn't get any service records, I don't know all of what's been replaced on the car. Visually, I can see that the alternator was replaced, and I know that the water pump was replaced, and that the A/C was converted over to R-134a some time in the past.
As far as I can tell, it still has the original A4LD automatic transmission. I can tell you from firsthand experience that yes, you DO want the manual trans if you have a choice. My A4LD is slipping a bit and the local trans shop says it's due for a rebuild, to the tune of $800 to $1,000. Maybe has 6 months to a year of service life left before it becomes undriveable. I'll swap in a manual before I pay to have the A4LD rebuilt.
All in all, the 2.3 is a bulletproof engine. I regularly shift at 5,000 rpms (Only after the engine is up to operating temp though) and the engine takes it with no complaints.
I've owned the Mustang for almost 5 months, and all I have done is change the oil and put gas in it. Speaking of, it's due now for another oil change.
As many people here will confirm, the Mustangs of this era and engine have chronic problems with a few areas, and a few key items to keep an eye on.
1) Replace the timing belt every 60k miles. If you buy the Mustang and have no service records regarding it, replace the belt for peace of mind and start counting off 60k miles.
2) These engines do not deal well at all with a shortage of oil or coolant, unlike some newer, much MUCH more expensive vehicles that can drive for a very short time to a service station under those conditions. Keep the engine oil and filter changed out, at every 3k miles. Flush your cooling system and refill it every year.
3) The automatic transmissions will also react extremely badly if the transmission fluid is low, overheated, or otherwise contaminated. Change the ATF fluid and filter every year. And also, avoid overheating, at all costs! These engines (and automatic transmissions, which share the engine cooling radiator) will go in short order if you beat on them in an overheated state.
4) For some strange reason, these engines seem to have negative reactions of varying severity to aftermarket (i.e, non-Motorcraft) spark plugs, wires, and ignition modules. When you replace any of these items, save yourself the headaches and buy the original Motorcraft parts. The cheaper aftermarket stuff is a bad deal in these cars.
Other than that, just do regular tuneups and maitenance (plugs, wires, belts, hoses, battery, wiring, distributor, air/fuel filters, etc...) and a 2.3 Mustang will most likely outlast its body.