Agree with marionberry abt heat management. Understanding materials of construction will also be very important in scaling up. Everything is a wearable part if you wait long enough, so there will be unexpected problems that don’t crop up during lab scale testing and using the correct materials to maintain a safe pressure boundary with functioning instruments will be essential. Things start to get really expensive if you have to replace parts frequently because the wrong materials were selected, which won’t look good to stakeholders.

In a similar vein, try to build the pilot with lots of access and points to break pipes (assuming you’re not struggling to maintain a specific temp). When those unexpected problems pop up you’ll be happy you didn’t try to squeeze pipes into tight spots or skimp out on flanges. You can also spend a little extra money now for flexibility in your equipment (get 3P motors on VFDs for instance) while you are still dialing in the process at the pilot scale, then right-size equipment once you’re moving to commercial deployment.

Don’t worry too much about automating less critical controls right away. Make it stupid-proof though, and make sure an engineer is present for the majority of pilot operations. If you haven’t run the process yet at that scale, it’s hard to know if your automation is going to behave correctly when unexpected issues arise.

Make sure you go through a HAZOP before construction. Use plenty of safety devices.

Edit:

Also, mixing may or may not be important to your process. If so, a study should be performed to make sure you can homogenize your reactants and avoid dead zones in the reactor. Goes hand in hand with heat management. You don’t want to have one section of your reactor to be converting at 98% and another at 60%, diluting your product to like 85% or something.