I've had very good luck with very short conserved intron sequences (e.g. 46 informative sites) for rather deep splits in cone snails exactly because the "fingerprint on the pipe" was so clear. The absence of conflicting sites made the phylogenetic signal super clear. So clear that my habit of using Spectral Splits was a formality.
I'd like to find many more of these sequences. Such seems to be the best case for very deep splits such as at the base of the eutherian tree with a comparable tree depth. Any ideas on looking not for extraordinarily long noisy sequences but for short sweet ones?