Piston width is measured by a large micrometer screw gauge and the bore measured with a bore scope, this is done because vernier calipers do not provide accurate enough reading. A bore gauge is inserted and then measured on the same screw gauge to determine clearance.
You might consider whatever the machine shop did as very hi tech - but infact it was very low tech and crude. The sad bit is that most of these shops are trying to keep each other (parts seller) in business too, hence they would recommend new expensive parts in about every engine job.
For the pump, its put up on a test bench and the fuel delivery checked on graduated cylinders, The pump is then spun to varying rpms to make sure the pump does correct fuelling at various loads and also cuts out fuel at the correct governor rpm. Ask around for good pump repair, You need to find a Denso shop that also has the correct data sheet to set the pump.
The nozzles should be adjusted and set and tested very very carefully for spray pattern before installing. Finally when the pump goes n the engine it requires a dial gauge to correctly time the plunger lift of the pump with engine at TDC no.1 after disabling the cold start system. Look up some videos for this. You will get the idea.
