What tires are on it? Some of those 2.8" plus tires are basically the same size as other brands 2.6" non-plus tires... Doesn't help with the 40mm rim though.
I enjoyed the 2.8" Rekon+ I had on my 27.5+ hardtail with a 35mm rim. It definitely still felt like a "big" tire and could get squirmy, but it wasn't too heavy, rolled well, and I never had any problems with flats.
Moved the nice 35mm wheelset to my wife's bike when I sold it--hers came with 2.6" Ardent Race tires on 30mm rims, but it was only a couple mm of difference when you actually measured them...despite being wider, the much nicer wheelset was a worthy upgrade.
So if they are nice carbon rims...maybe the 40mm wouldn't be too crazy even if you went down to 2.6" to open up your tire options? The 3.0-3.2" side of plus may be completely dead, but I think the 2.8" side almost lives on and has expanded selection: they just call it 2.6" now.
As for the 29 conversion, I'd make sure it actually works--it was common for the earlier plus bikes designed around the 3+" tires, but some of the later models with 2.8 tires weren't meant for it and would probably ride just fine if you dropped to a narrower 27.5 rim and smaller tire.