Actually, I have no relation to SHO Shop, other than that they are in California where I was born. I know several SHO owners who have used their stuff in the past, and I have had conversations with them regarding my SVT. I've also talked twice to Joe at SP Motorsports. Of the two, I'd say SP has a better clue regarding SVT's. This is based on responses to technical questions. SP also has a conection to the SHO shop, based on their parts sales. I can't speak to too many of the other parts houses, as I didn't see much to what they were offering.
At present, my Contour is fairly stock, but that's because it just came out of warranty. I'm planning on the ST200 intakes, and a SHO Shop h-pipe (the car needs to be every-day driveable). Most of my hot-rodding experience has been on more traditional engines (small block Fords and Mopars, turbo 2.3's, and 5.0L's), but the SVT's are still engines, although a bit more complex than a '70 Ford.
The 3.0L change makes more sense to me than dropping a used motor in, since you don't know the history of the used motor (oil changes? beaten on?) The 3.0L gets the new short block, as well as additional displacement (I was raised on the mantra "there ain't no replacement for cubic displacement"). You're spending money, but at least getting more than you started with.
As far as the dealership telling you several hundred dollars just to diagnose the problem, something is really wrong. What are the symptoms? Metal in the oil? A hole in the side of the block? Oil in the coolant? Won't turn over? What was happening when it died? Piston condition and lower block conditions can be checked with a borescope. Why several hundred dollars? The answer is that they don't feel like doing it. If its a spun bearing, it may be repairable. What makes them think that you need to spend $4500 to put in a new 2.5L? Answer - repair is not as profitable. Mechanics get payed based on a job time factor multiplied by the labor rate of the dealership. Wanna bet that the replacement has a juicy time factor, while I&R doesn't? What's the dealerships take on the new engine from Ford?