The first part of the Sandpit (or even before) should map out the range of existing and near term technologies that help provide control of matter at or near molecular scales. Then assess the current capabilities and best near term improvements that can be made in each. Then brainstorm around how they might be combined into complimentary systems.
You would need to specify the dimensions of control that you would have. Size ranges of control, degrees of control, reaction control, speed of processes, repeatability of reactions etc…
self assembly and guided self assembly
magnetic and electrical manipulation
STMs, AFMs, TEMs
Dip pen lithography (arrays of 55,000 and plans for a million)
Look at the sensor technology
Supercomputers and quantum computers