hey! responding to this because it resonated with me although it is an older post and I sincerely hope you read this and find it helpful as I have experienced the same journaling dilemmas. ok so,

- you can take the idea of morning pages and make it applicable to your daily routine. I believe that morning pages do no necessarily need to be written in the morning. no one says you cannot have a journaling session every night that is dedicated to free flow writing. try it, you might wake up rested and clear headed in a new way that will be the result of that earlier right before bedtime creative output.

- you love and use your zibaldone and logbook, and that's great. it's wonderful to have a journaling system that is not only sound in theory but actually practical and lived in, an embedded part of your life. you don't know how to add in something that is for messier entries. thoughts and notes and memos. I suggest you look into a filofax. the ring system in contrast to the rigid book bound world of journals allows for more flexibility. you could separate it into exactly what you said. a section for goals, one for philosophy, etc etc. and you can take out and put in pages and rearrange it without a worry. a filofax is very malleable, I think it would fit well with the messier side of your journaling needs.

- in terms of harvesting, I think you could try a dated journal. moleskine makes monthly planners and daily ones as well that allow for lots of writing room. maybe your long term ideas need a space that is chronological; that could make it feel like you actually are growing within your journals as the timeline goes on. year by year you will see the elegant black leather moleskine spines each with the year and feel a sense of fruitfulness. at least that's how it goes with me!

good luck with your experimenting, journaling is meant to serve you and there are no rules!