In 1992 there was an initial 'part facelift' which included the so-called 'Sacco panels' on the body for the first time. The new engine range was launched in these cars - every motor was significantly changed or a brand-new design. In Europe there was a choice of two 4-cylinder engines, one 6-cylinder diesel and two 6-cylinder petrols. The US also got a V8 in the range, as well as the famous limited edition Porsche-built 500E.
The full face-lift arrived in '93, and included along with the differences you mention, new interior fabrics, a new range of stereo options and a move to 15" 8-hole alloy wheels as standard in place of the previous 15-hole style.
The cars were also re-badged at this point, with the 'E' prefixing the engine designation as it still does today, and the cars became known as the 'E' Class as a result.
Unfortunately there were some changes for the worse, largely due to MB's ground-breaking attempts to 'go green'... water-based paint was first used in '93, as were catalytic converters and 02 sensors on the new engines which obviously aren't as cheap or easy to replace as the old-style exhaust systems. Worse than this, a bio-degradable material was used in the manufacture of wiring harnesses across the range, which on most cars have prematurely degraded causing all kinds of minor and severe running problems including expensively blown ECU's. Many surviving cars have had the harness replaced, budget for it if you buy a car still with the original part.
I think for these reasons, many believe the pre-facelift cars represent the true old-school Mercedes values of longevity, toughness and mega-mile reliability, but it has to be said that the later cars make up for their failings with far more modern, economical and powerful engines, all of which are highly regarded for durability. I have not noticed a difference in out-right build quality between the older and newer models, and personally I feel the newer the car, the better (all else being equal) as there will be more life left in all those components that are affected by age rather than just mileage.
The 5-speed autos are very nice to drive, maximising the engine's performance with top gear being effectively an overdrive that allows amazingly relaxed cruising. However, they have a poor reputation for failure over here as compared with the bomb-proof 4-speed boxes that can often last the life of the car without a re-build. I'm afraid I can't enlighten you as to why they fail, just that many failures have been reported over the years. Not sure what US cars were specified with, the info will all be here somewhere.
Euro models could be specified with manual gearboxes from the model's launch in 1986 across the range - many European buyers would never consider an automatic car, especially in any of the entry-level models. Auto gearboxes still represented the most common choice in the case of W124's though, as they suited the nature of the car far better... MB's manual 'boxes were not well liked by reviewers or keen drivers - they were far from a pleasure to use when compared to the contemporary offerings of BMW say, or Audi. With miles and age they get worse, and a manual 124 will now most likely have a rubbery, imprecise feel to both shift and clutch action that for many is not acceptable, unless perhaps it was an early taxi-spec 250D. The auto 'box was still regarded as an option rather than as standard over here. Ditto leather seats, alloy wheels and AC - many Euro models were ordered without these options as well.