...So I checked spark with the plug wires with a path to a metal plate and cranked the engine with the starter button. Im getting spark on all 4 leads !!!
When I put plug caps on and spark plug on Im not getting spark except for cylinder 2.
I cleaned the plugs ( they are 50 km old) and no spark.
Im stumped because before I got that short the bike ran perfect. Before I changed the RR i did blow a fuse but after replacing it it ran perfect.
Could the short damage the plug caps or spark plugs ? Or is the spark too weak?
That is strange. If they are resistor-plugs, they do sometimes fail in a way that prevents spark. I've seen that quite a few times, but 3 plugs at once would be strange. Are the plugs 50,000 miles old, or 50 kilometers old?
I would expect the reg/rec/battery short to cause the plugs to be affected at all. Bad plug-wire caps can have a similar affect to bad plugs.
Definitely try new plugs and make sure they fit into the plug-wire caps properly. That is, make sure the plugs are with or without the screw-on terminal top depending on what your wire caps require (as Mikaw explained). If everything is not secure and clean, the spark can sometimes travel along the outside of the spark plug to get to the engine. When this happens the cylinder won't fire, but when you check for spark you will get it on all 4.
Still, none of the above would be caused by the charging system short.