I'm not clear on why you need a PDF at all if you have the data in an Excel file which can then be imported into a table or tables in your database. Is this a scanned image of the actual hard copy document completed after the mission perhaps?
Otherwise, I don't see the point to using a PDF.
With regards to:
how do I get data from the portals in the Missions layout into my MACR layout.
From what I see, you have a Missions table with a relationship to a table that uses one relationship or another to list the aircraft that participated in that mission. I would set that up with a many to many relationship between a table of aircraft (where there is one record for each aircraft) and a table of missions by using a join table to implement the many to many relationship. If so, then this portal would be to the join table. Is that what you have here?
Presumably, an MACR would be linked to that same record in the join table, so clicking a control in the portal row to see the MACR for that aircraft in that mission would be a case of using that relationship to pull up the records (imported from Excel) or the PDF for the MACR (inserted into a container field).