Welcome to the farmOS forum @Jeff_Piestrak and @JustinP! 
I’d love to brainstorm agroforestry record keeping conventions in farmOS with you both. We can either start in this thread, or perhaps a quicker kickstart would be to talk about it on a weekly dev call or monthly community call (and then summarize the outcomes here).
Couple of quick thoughts in the meantime…
Cool so the first step might be to create some Land assets to represent your land and the land of others that you’ll be tracking (all within the same farmOS instance).
The next decision to make is what granularity of record keeping you’ll need. Do you need to track activities/inputs/etc to individual plants? Or just groups of plants?
Either way, you’ll want to create Plant assets to represent each “management unit” you’re tracking (whether that be individuals/groups).
I assume you have some plants that already in the ground? As well as plans to grow/buy and transplant others? Do you have records of when the “already planted” trees were transplanted/grafted/whatever?
Ideally you will have 1 Plant asset for each individual/group you are tracking, as well as 1 Transplant log with the date and location it was transplanted. farmOS uses logs to give assets their location (see Movements and location | farmOS).
This may seem like a lot of records (especially if you have hundreds of individual trees and you want to track each separately!) - and it is! That is why I said above:
The next decision to make is what granularity of record keeping you’ll need.
The more granular you get, the more records you need. 
So, if you want that level of granularity, you may also want to consider a CSV importer to help you get data into place from a spreadsheet to get started quickly. @paul121 and @Symbioquine are working on a blog post right now that demonstrates a simple CSV importer Python script (and there are other forum topics with more detailed examples). The blog post will most likely be published soon, but here is the PR in progress if you want a sneak peek: Create a post with a quick farmOS.py tutorial by symbioquine · Pull Request #14 · farmOS/farmOS-community-blog · GitHub
Once you have all your assets represented (and their locations mapped), then you can really go to town tracking more kinds of logs: inputs, harvests, observations, etc - whatever you’re hoping to track.
Happy to think through the details of those as you get into it!
There have been a few similar forum threads about this kind of stuff… I encourage you to use the search feature, and feel free to cross-post links to the relevant topics/comments you find in this thread so that it makes it easier for future readers as well. I’ll try to do a quick search myself and post what I find…