First of all there are no significant differences between lag experienced on a stock ROM to a custom ROM, even with a custom kernel. In my view, all perceived improvements are very marginal and seem to detract from the real issue, which seems to be processor related and linked to the JB 4.3 system builds that Samsung issue.
If you look around most people experience lag with JB4.3 based ROMs on Samsung models with the Exynos processors but hardly any with models using a Snapdragon. I have two Samsung Exynos based phones, a Note 2 and a S3 and both struggle to a greater or lesser degree with lag, irrespective of ROM (stock based or AOSP/AOKP/CWM) and custom kernels. Since 'upgrading' to JB4.3 I have never been able to completely eradicate this problem. In that regard, JB4.1.2 was miles better.