Yeah, I would suspect the CG moved forward with the heavier engine. This would require up trim for level flight, and could cause the nose up on downlines. But, he says it also pitches up at low throttle on landing approaches as well, a nose-heavy plane would not do that.

I seriously doubt the thrust angle would cause any problems on down lines, the thrust angle affects the up lines more.

The Extras have a pretty high thrust line, and that (I think) can cause a pitch up on down lines, from the braking action of the prop. I think the down-mix at low throttle is probably the best fix.