Where are you going to find a decent B6? I would have thought that these days they are in the same category as rocking horse sh!t ... ? I am sure there are a few around, but 'decent' ones might require a lot of looking. And search here for 'small nose crank' problem, something that has killed a lot of the early B6 engines and which may not be easily identifiable on a non-running engine. The best option for finding a 'decent' engine would be to talk to ALL the MX5 workshops you can find across the country (literally) and see if they have, or know of, engines that have been pulled to replace with BPs (or even another B6). You will pay a premium , but the chances of getting an engine with a known history are improved, and you can still fall back on the junkyard option if that doesn't work out.
You don't want to be paying someone a $k or so every so often to slot in a another one, even if you get them cheap, and DIY will get tedious quickly. As well as purchase price, a timing belt service (~$1k) would be requirement if no service history was available for the engine.
I'd suggest your minimum budget would be price of engine (no idea, say $250-$1K), $1k labour to fit, and $1k for timing belt service (may be a little cheaper if the engine is out of the car) if required. So ballpark estimate, low $1250, high $3000.
If the car is to be a keeper or long term ownership, I'd look for engines without woodruff key damage (aka short nose problem) first, then pick the one that looked the best buy for a rebuild, and do a rings, bearings, valves job. That should do you for another 300,000kms and add (guessing) ~$2k to the bill, but you haven't paid a premium for a 'decent' engine, so the price would be around $4.25k all up.
You could save the cost of the 'new' engine by rebuilding the one in the car, but without knowing what condition the crank, rods, etc are in, I am hesitant to suggest that. Buying a good rebuild engine is likely to be quicker and cheaper than spending money to find out the blown engine is not suitable, and then chasing the rebuild candidate.
