Generally when an engine runs, if it is running lean, it will run hotter. If an engine is running rich, it will run cooler. Each individual cylinder is no different. After an engine is completely warmed up, if one measures each cylinder at the same basic place on the exhaust manifold, you can get an idea of which cylinder is running lean and which is running rich in comparison to each other.
On the GM LT1 (Gen-II Small Block) ECU, there is a table in the ECU called the Individual Cylinder Fuel Trim Multiplier. I don't know if every ECU has one, but will assume for the sake of argument that they have something like this. This table allows for the fine adjustment of each cylinder to get them working at the same levels. To factor this and get the table adjusted correctly, you need to take the temperature of each cylinder at the exhaust manifold.
To perform the operation, you take the temperature of each cylinder (as you stated you did in your question), then make adjustments in the table to compensate. You need to choose one cylinder to work from as your base. In most instances you'd take one of the interior cylinders (in your case either cyl-2 or cyl-3). Once you have established your base, make adjustments to your table to add fuel if it's too hot or subtract fuel if it's too cool. This process could take several iterations to get right.
There is a case where certain cylinders may be starved for fuel. In this case, those cylinders would be far cooler than the others due to lack of combustion. In that case you may consider fattening up those cylinders first to alleviate the issue.
The theory with adjusting the cylinders to match is if each of the cylinders are working at the same output level (heat output in this case), they are each producing about the same amount of power and therefore are working in concert with each other. This produces better engine harmonics and will help with longevity. It can also help with gas mileage.
For the LT1 engine there are tables for both idle and off-idle. This will allow for even finer engine tuning adjustment.