I reckon you are overestimating the amount of players going on Lions tour, and selecting too many rookies in one side. I would select a few players with a bit more experience such as Paul James, Hibbard. Also have players like Dan Biggar given a chance. That side looks more like a midweek side.
Remember Japan will be stronger than perhaps most expect, unlike other Tier 2 sides who have most players based in Europe, Japan get all their players available no problems as nearly all their players play in a JRFU run league and can get much more preparation time compared to say Samoa who would only get their players a few days beforehand. Japan will have had a whole Asian 5 Nations to prepare and test out combinations and familiarity if against weak opposition. So I expect they will be a tough side to face, they nearly beat a strong Samoa side in June by the way blowing a 16-0 lead. So Wales can't take this lightly and liberally throw too many experiments in at once. Saying that though there is more chance to experiment compared to normal.
A big weakness of Japan is their scrum, which is why I would make sure Paul James plays to make the best advantage of this area. Hopefully Craig Mitchell will be available too. It is also a good time to debut Samson Lee imo.
I hope there are no undeserved caps on this tour though, Rhodri Jones and Harry Robinson are two players who in my opinion I haven't seen do an awful lot yet get selected for Wales. Until Harry Robinson gets past Tom James in the Cardiff Blues side he shouldn't play for Wales imo. Eli Walker, Tom Prydie, Richard Fussell are on better form. As for Rhodri Jones he was seen as a utility prop I think at one stage, but now with 23 man squads there is no need, he needs to get back having game time with his region, last time I saw him play he was destroyed by Leinster. Gill and James should be far ahead of him, given both of their credentials shown at H Cup level.