I had an opportunity to work on a similar kind of initiative - during due diligence phase to be precise. Later, it was handed over to my peers to take over. However, to my knowledge more than 90% of my recommendation(s) presented in the due diligence report were considered. Hence, here is my insight on streamlining the project management capabilities for a Research & Development facility.
Consider capturing the historical summary information from your Research and Development Information System (RDIS - if you have the information as a system) data (the more the better; but three years should be fine) in a spreadsheet to analyze the current scenario. Otherwise, you will have an opportunity to create the system.
Summary Information: You could segment the information into four phases such as Conceptualization, Planning, Implementation and Completion. Within each phase, you could include the key constraints such as Funding, Schedule, Cost, Risks, Time, Resources, ROI, and many such columns as you require.
Under each constraint(s) you will need to further decompose into various columns such as budget, planned, actual, variance. At times, you might not know the budget and planned information, you will need to find out from your colleagues or from the respective department heads.
To visualize the information, it could be something like this:
Based on the information you have gathered in the spreadsheet, you will need to analyze every data point. For example, you might have a line-item having good funding but did not yield as expected. Here is where the meat is. You will need to further your understanding on the "why" part; you could use parametric or could brainstorm with the stakeholders.
Keep updating the spreadsheet as you move ahead. You see now, you will have a full view on what's working and what's not and why is it working.
Understand the proposed goal and reinforce to arrive at the stakeholders input quantitatively. This means, when they say, ' more aggressive and more practical approach', capture it quantitatively. Capture the goal very succinctly - mostly in-line with the summary spreadsheet.
The next step shall be to discuss with your department users or with the research assistants to arrive at the work breakdown structure (WBS). By creating a responsibility assignment matrix (RAM), you will further gain a proper understanding on who the owners are and whom to approach if you face challenge.
This WBS along with RAM shall remain as your key input and template for any of your R&D projects you plan to kickoff.
Gain understanding on Earned Value Management (EVM) if you do not have. Otherwise, if you have the exposure or experience in using EVM, then almost all the key metrics can be arrived at using this wonderful tool.
It will help you immensely for reporting; you could use it for all kinds of reports - status, performance, forecasting, etc.
Now, you will have sufficient understanding on the business process. This will help you to decide on whether you will need to apply traditional project management or Agile for the goals you set.
The next step shall be to apply the right framework and follow the rulebook.
BTW, please ensure you will need to keep monitoring and controlling and tweaking to ensure you achieve the R&D goal.
Hope this helps you to proceed further. Should you need more information, please feel free to shoot your questions.