After seeing your log, I withdraw my suggestion of using Rejuv less, your spell distribution looks perfectly right. Your problems come from having to heal more than the two healers can (or, almost). I've never seen such ridiculously low overhealing (for a druid), for example 10% OH on Lifebloom means the Tank is never at 100%. You're pulling that Shaman through (he could at least use his CDs better), and your raid is taking more damage than necessary. Only thing to improve might be LB uptime, you'd get a lot more CC procs which reduces mana problems.
About Spirit, it's certainly better for you than for me, because your fight was 1.5 minutes longer. However, especially in this zero-overheal situation, 1000 more int do a lot more for your heals than the same amount of spirit.
Jin'ya certainly is good as a healer. Might not be the best in slot, but you're doing nothing wrong upgrading and gemming it.
---------- Post added 2013-02-07 at 12:54 PM ----------
Actually it's much worse, I had remembered the numbers wrong. Spirit Flask lets you cast 2 extra Rejuvs EVERY THREE MINUTES. It is really that bad. If you want to read more on that topic, I suggest this article of one of the top resto druid theorycrafters:
http://iam.yellingontheinternet.com/...ling-problems/