They might both be Ford Focuses, but they're a couple of generations apart meaning that they are not only physically different, they also used different transmissions to each other. Even if, by some miracle, the older gearbox would bolt to the newer engine, the car still wouldn't have the correct electronics to make the transmission work properly.

Even if the transmission in question was a manual which requires much less in the way of electronic control, the unit in the 2008 Focus was a five-speed, while the later car used a completely different six-speed. Even things like the clutch and flywheel would be incompatible. You'd probably even find the gear-shifter for each transmission enters the cabin in a physically different spot, meaning the interior trim would no longer fit.

Don't be so sure your car isn't covered by Ford's factory warranty. If it was delivered brand-new (as opposed to built) after May 1 of that year, it's subject to a five-year/unlimited kilometre warranty, so would still be covered. However, if it was delivered before that date, the warranty would have been three years or 100,000km which has now run out. Even so, given the kilometres and the service record, I think you'd be a good case to have Ford come to the party with some help on the repairs on a pro-rata basis.

From what you've told me, I'm guessing you've only dealt with Ford at the dealership level. Go over their heads and talk directly with Ford HQ's customer service department. A quote for $3500 just to examine the car is, on the surface of it, absurd and should be treated with suspicion. Any competent mechanic should be able to diagnose what's going on and whether or not the engine needs to be replaced. My advice here would be to have the car inspected by your state motoring club (the RACV in Victoria) which can give a cost-effective and independent report on the car's condition (and won't cost anything like $3500). This is also excellent legal and evidential back-up if the case does progress to VCAT.

On the face of it, 62,000km is not a reasonable lifespan for a fully serviced engine and the manufacturer should shoulder at least some of the cost of putting it right. Your last resort should be to contact the ACCC and talk to that body regarding your rights under Australia Consumer Law which covers goods (including cars) that are not built to a reasonable level of quality or are unfit for service. A failed engine at such mileage may well fall into that category.

Try a Toyota Corolla, Mazda 3, or a Ford Focus. All would seem to fit the bill.