I’m no Mac expert, but.
I can readily see why a motherboard swap might cause instability. Different ages / revisions of motherboard could well have a different mix of chipset components on there, and even with an otherwise like-for-like swap you might still have differing firmware revisions or other ephemeral changes. Whilst it’s not ideal, I’m not wholly surprised that Apple are suggesting a clean reinstall of the OS, this sounds sensible to me.
With respect to the OP, I’m sceptical of statements like “this has been going on for six months”; how much of the six months have been Apple’s fault, and how much of it has been the OP putting up with the problem and refusing to follow their advice? (I don’t know, of course, I’m guessing here)
Also, “it’s business critical” holds no water I’m afraid; if it’s critical, you build in redundancy. If a faulty PC was impacting my business to a point where I was losing money, I’d buy a new one and keep the old one as a spare. Whether you use it daily for your business or twice a month to download porn matters not a jot as far as either Apple or warranties are concerned.
That said, if I’d had it back several times without success I think I’d be squealing Sale Of Goods Act. I’d suggest that it’s reasonable to expect that a two grand laptop still warrantied by the manufacturer should last for the length of the warranty, and you’ve given them reasonable opportunity to rectify the problem and they’ve failed. You really need to try a clean build though, you’re on shaky ground until you can disprove it’s a software issue (which when all’s said and done, it might be).