The 'a' is angular acceleration so there must be a change in rotational speed involved. Starting with the second part of the question, first:
If you spin the crank and remove the drill, the rotation will slow to a stop owing to friction. You can measure the torque required to turn the crank in the bearings with a torque wrench or other method. Spinning the crank up to drill speed and then removing the power and measuring the time required for it to come to a stop would permit you to calculate an angular de-acceleration.
You can also roll the crank down a couple of inclined ramps under the main journals and get a time to descend owing to the force of gravity. There are also formulas derived from the pendulum formula.
Perhaps the best compilation of methods is in 'A Handbook of Torsional Vibration" published by Cambridge University. This 1950's classic has been recently reprinted.
Which brings us to the first part of the question and data logging. The periodic inputs of the piston(s) through the connection rods do cause accelerations of the crankshaft ans subsequently slow the rotation during intake, compression and exhaust. The flywheel is designed to have sufficient rotational inertia to absorb and release energy so that the change in speed is kept to a small percentage of the average crankshaft speed.
The flexible nature of the crankshaft can result in some torsional (twisting) vibrations of the crankshaft. You may have noticed vibration dampers on the ends of some crankshafts.
Your data logger will pick up these vibrations along with the torque pulses. The friction and forces of compression act on the crankshaft and your data logger will reflect this slowing action. The inertia of the dynamometer or engine loads also act on the system.
The 3D software can produce a number that should be as accurate as any.