One thing to note is the manufacturer used IDC type plugs because they saved a ton of assembly time. You will never see IDC in high reliability (e.g. spaceborne) equipment - there's a reason.
However, with the light use that most home based pinball machines will see - you would probably be ok with IDC's as long as you buy the correct size (connector MUST match wire size).
The best connectors and contacts you can get on there are the Molex polyester 41695 series plugs with their high current box contacts (45570 series). These are now good up to 13 amps but tend to be a bit on the pricey side. Most people just end up buying the nylon plugs with trifurcon contacts... Again, decent contacts that will still last a long time.
Biggest killer of these connectors (both IDC and crimp on) is the mating/unmating cycles. These have a VERY limited unplug/replug cycle count before they start slopping up, building up resistance and then building up heat.
I normally only worry about headers if the original plating is bad. If no longer bright, shiney and even then it has seen heat and can become a potential future problem.
Do not solder contacts after crimping them. The solder *will* wick up under the insulation and will create a rigid zone at the back of the connector. This just screams "break me here!".
Ed