The below are all how I do this, rather than "This is the RIGHT WAY!"
My view is that if you support all possible nuances and complexity, you will add so much complexity to your system that it will be unusable. So you have to strip out complexity until it's usable. Exactly what you strip depends on your work, your work style, the tools you're using (I agree that switching to a tool that does this linking automatically would be a good idea), your mind, and your personality.
The below describes what I strip out right now.
1) I think that converting emails directly to tasks is a mistake. I know that lots of people do it, but for me, it makes a mess. A single email may contain many tasks. A single task may be represented by many emails. The email may contain several paragraphs while all you want when scanning tasks is a few words.
So when I get an email that will probably be a task, I enter it as a line item in my OmniFocus Inbox. If I had a paper system, I'd scribble it on a paper scrap, and throw it in a physical Inbox. And I include enough information to allow me to search for the email. Then I just stuff the email into a single archive with all the other emails for the year.
Examples of the line items/paper scraps:
Bug in Widget report totals. (Email J. Smith, 3/13/16)
Suggestion from manager re new hires. (Email 3/7/16)
Policy change re Take Daughter Work Day (Email 2/15/16)
When you do this, you have a list of items, instead of a floundering mass of emails. That is, IMO, much easier to sort and, once sorted, much easier to scan. It feels like extra work compared to just dragging the email or running a script on it, but IMO it pays off the first or second time you re-read the email to figure out what in the world it was about.
3) I don't do sub-actions. Either the "sub" thing is a separate project, or it's just an action of its higher-level project. So while someone who does subprojects might have:
Throw Grandma's birthday party.
-- Deal with food
----Ask Jane for recommendations about caterers.
----Another action.
----Another action.
----Another action.
----Another action.
-- Find venue.
----Call the community center for rooms and rates.
----Another action.
----Another action.
----Another action.
I would have EITHER:
Throw Grandma's birthday party.
-- Ask Jane for recommendations about caterers.
-- Call the community center for rooms and rates.
OR:
Deal with food for Grandma's birthday party.
-- Ask Jane for recommendations about caterers.
Find venue for Grandma's birthday party.
-- Call the community center for rooms and rates.
I realize that all of these are essentially the same thing, but to me it makes a big difference in hair-tearing to avoid that intervening hierarchical level.
4) Notice how all the "Another action." went away above? I don't allow more than a couple of actions per project. Ideally, I'd have only one.
If I fear that I'll forget the other actions, I'll put them in an unsorted list in the project support material for the project. But more and more, I'm learning that if I can think of it today, I'll think of it next month.
So, if I could make my Next Action for a project any one of sixteen possible options, because none of the options depend on the other, which one do I pick? I just pick one. I wouldn't say it's random, but it's pretty close. If next week is a meeting-heavy week and I can't face another meeting, it'll be the non-meeting task. If a coworker who's always travelling is in town next week, it'll be the task that depends on him. Unless I don't like him and it's going to be a stressful week. I just...pick one.
5) I put most projects in Someday/Maybe. If I'm not going to work on it in the next two weeks, or even if I MIGHT not get to it in the next two weeks, it's in Someday/Maybe. If it's in Someday/Maybe I don't even scan it on a daily basis.
6) The end result of this is that I want my Next Action list to be no more than about a dozen items long. There's Someday/Maybe and project support material ready and waiting if I run out of work, but my scan-it-now list is as short as I can possibly make it.