Relational Answer
This is in case you want a Relational Database, with the Relational Integrity (as distinct from Referential Integrity), Relational power (at your level of question, that means JOIN power), and Relational speed, that Record Filing Systems (typified by Record IDs as "primary keys" in every file) do not have. That is all I provide.
You can't model anything when your starting position is spreadsheets of what you think, with an ID field stamped on each of them.
In addition to that problem, ID fields create many others. Please read this Answer from the top to False Teachers.
Yes, too many n::m tables is bad. In the sense that it is a red flag indicating that the data is not fully Normalised. Which of course, must be completed before anything else is done.
Try this, this is what I think you need, given the spare requirements (feel free to be more specific).
Workflow Data Model
Data Model
That is an IDEF1X data model. IDEF1X is the Standard for modelling Relational Databases. Please be advised that every little tick; notch; and mark; the crows foot; the solid vs dashed lines; the square vs round corners; means something very specific and important. Refer to the IDEF1X Notation. If you do not understand the Notation, you will not be able to understand or work the model.
IDEF1X data models are rich in definition, something that UML and other diagrams cannot even approach. Refer to Data Model Anatomy for assistance in reading the data model, a different perspective to the Notation document.
Solution
Look at the Current Step Only model, and get your head around that, before contemplating the History model.
Compound Keys are standard fare in Relational databases. In fact that is the only way to obtain Relational Integrity (as distinct from Referential Integrity) and you need all the integrity that you can get in this scenario.
See if you can code from the model, and obtain all the reports and queries that you need, with a single SELECT each. If you need help, please ask.
Please feel free to comment or ask questions.