You'll have to remove the caps or caps and plugs wires as an "assembly" to measure through them. Stock plug wires should be plain copper core non-resistor wires so measuring through them along with the cap shouldn't affect the reading. The stock plug caps have a rather odd rating of something like 8K or 9K ohms. What happens when they start going bad is that resistance starts climbing. Eventually it gets so high it starts choking off the spark. Higher RPM operation can sometimes push through this higher resistance but lower RPM operation may not. This could be your problem.
If you haven't done so, it's probably a good idea to make all new, fresh connections between the plug wires, caps, and coils. Trim about 1/4" off both ends of your plug wires to get to some fresh wire. Then strip about another 1/8" of the insulation off and fan the wire strands out in a radial pattern like so .....
This will insure good contact and a good connection between the wire and cap or coil. If you look inside the end of the plug cap that goes on the wire, you will see what looks like the pointy end of a wood screw. Basically, you "screw" the cap onto the wire. At the coil, you may find the same wood screw looking thing but many times it's just a pointed metal pin, like the end of a nail. With that, you just push the wire onto it.
If you haven't done so, it's probably a good idea to make all new, fresh connections between the plug wires, caps, and coils. Trim about 1/4" off both ends of your plug wires to get to some fresh wire. Then strip about another 1/8" of the insulation off and fan the wire strands out in a radial pattern like so .....
This will insure good contact and a good connection between the wire and cap or coil. If you look inside the end of the plug cap that goes on the wire, you will see what looks like the pointy end of a wood screw. Basically, you "screw" the cap onto the wire. At the coil, you may find the same wood screw looking thing but many times it's just a pointed metal pin, like the end of a nail. With that, you just push the wire onto it.