I just took the caps off for some testing. #4 read 5.01k ohms and #1 read 4.89k ohms. #1 looks a little low, could this cause a problem?
No. You have 5 K ohm resistors and the tolerance is about 20% of rated value. Your caps are good. When they break down their value usually goes up. They can even open, creating an internal spark gap that wastes energy. Some caps are valued at 10K ohms. and others have been available at 7.5K ohms, though it has been a while since I've seen those. You can get them with no resistors in side too, 0 ohms.
I asked you to check them because an open cap entices the spark to occur where not expected.
I did not notice any black gunk on the wire tips. When I take the #4 cap off when while the bike is running, I can feel the spark through the wire. Is this normal? Any more thoughts?
Yes. 1 and 4 fire simultaneously. And, the current flows from one spark plug through the other. It will use you as a path if you get in the way, or if you provide an easier path than the spark gap jump.
Are you still getting a spark jump to the engine? If the spark is jumping through the wire insulation from the internal wire, then it is defective. If it is traveling along the outside of the ignition wires, there may be some surface contamination providing an electrical path. The last thing I can think of to try before replacing wires or rubber bits, is to clean them off with, alcohol, or MEK and let dry thoroughly. You need a solvent that will clean contaminants, not leave a residue, and not dissolve the insulation.
Dust that has been used to pass an arc may leave behind a carbon trail. Such a trail is conductive and provides a path for the electrical current. You do NOT want anything conductive on the outside of the ignition wires.
Cheers,