I'm running years 1-4 on 1-7 collection and wonders if the time includes the cutscenes because there are alot of them and most take a little while or is the cutscene times taken off at the end?

Also playing 1-7 collection can I submit runs for both years 1-4 and 5-7 separately or do I have to submit a run for all years only?

To the first part, the cutscenes are included in story mode as we can't skip them. Anything on console has the unfortunate disadvantage of being without a load remover. To the second part if you are doing runs on the 1-7 collection you would have to submit to the two different games. 5-7 is currently being reworked to better accommodate these new things

or if you want you could go to the 1-7 board: https://www.speedrun.com/lhp1-7. of course the categories are long, so...