Incase anyone comes here looking I was able to get the 100% and based on my experience this is what it required. From the above, what I was missing was a hidden recipe in the Data>Stuff Items section.
Tracked Data that contributes to 100%:
Completing all story missions.
Getting all mutations (including reliable friend, No max levels required)
Discovering all points of interest on the map (98 locations)
Unlocking all creature cards (59 creatures, only 20 gold required for trapper peeper mutation)
Unlocking and purchasing all recipes from BURG.L/ASL Computer.
Finding all Wendell Data items (65 items)
Finding all Ominent Data Items (15 items)
Finding all BURG.L Data Items (15 items)
Finding all Stuff Data Items (16 items, this includes the 5 hidden recipe notes in the yard, 4 password notes, 4 chest keys, and 1 assistant manager badge)
Completing all MIIX.R's (5 regular, tracked and mapped locations)
Untracked Data that contributes to 100%:
Finding all regular Milk Molars (74 molars, should have 2 left over after maxing out)
Finding all Mega Milk molars (45 mega's, should have 0 left over after maxing out)
Finding all SCA.B Schemes (48 Schemes)
Defeating Main bosses (2: Brood and Mant)
Level 15 Brain power (from analyzing items)
Completing the Super Mix.R's (3 locations located in upper yard, not marked on the map or in data/places section)
Things that are not required to get 100%
Raw science nodes. You do not explicitly need to collect all of the raw sciences nodes outside of needing them to purchase all of the recipes from the BURG.L/ASL computer.
You do not need to get all gold creature cards (you do need 20 for the Trapper Peeper mutation)
You do not need to max out your mutations
You do not need to discover all recipes
You do not need to discover all trinkets
You do not need to discover all rotten items
You do not need to complete all BURG.L Mini quests
You do not need to tame or have pets
You do not need to discover and analyze all items and resources
Hope this helps anyone on the verge of insanity like I was, stuck at 99% haha.