You need to use a specific tool to measure the cylinder. It's called a bore gauge. They usually come as a set and can cost from around 50 bucks to well over $200. The more expensive the set, the better they seem to work, to a point.
Take the measurement with the gauge in line with the connecting rods. Measure at least three places in the bore; top, mid, bottom, and then measure three more times at 90 degrees from the first measurement. That will give you an idea of whether the cylinder is round, tapered, or oval.
Your machine shop should have checked for out of round when they worked on your engine, as it's a pretty common measurement when seeing what is necssary for a rebuild. If you do go over-bore, you will need to send the cylinders off, as most shops won't be able to bore the nikasil and re-plate it .Nikasil is a plating and is very hard. The plating is not very thick, and if it is bored out, it exposes only aluminum underneath, which cannot hold up to the combustion process. Millenium Technologies and US Chrome are two places that have good reputations for doing good work, replating and repair are their specialties. Usually, the cost is about half the cost of a new cylinder.
If your cylinders are out of round, you can also send them off and have them bored back to round and put back to the OEM size by those companies. Send them the pistons/rings and they will set up the piston to the cylinder which saves you a step.