What you probably want is Aegisub - just line up the Japanese subtitles with the audio from the video manually.
Problems like this are usually caused by ad breaks that are still in the Japanese subs but cut out by whoever encoded the video.
I've never had any major trouble with the English/Japanese subtitles lining up after fixing things with Aegisub - subs2srs seems to deal with it quite fine even if things are broken up differently by the English subbers (or maybe it doesn't but I just don't notice, but it's never an issue in any case).
Problems like this are usually caused by ad breaks that are still in the Japanese subs but cut out by whoever encoded the video.
I've never had any major trouble with the English/Japanese subtitles lining up after fixing things with Aegisub - subs2srs seems to deal with it quite fine even if things are broken up differently by the English subbers (or maybe it doesn't but I just don't notice, but it's never an issue in any case).