Intermittent Spark/ Battery is not charging

[Canal rat]

I have a 91 VE200SLEID that takes a while to spark when sitting for a few days. Once she sparks it will go all day on the water. History: The guy before me put in new power pack & starter. I put in last fall new rectifier/regulator, 4 gauge cables, water pump and this year a 800CC Interstate battery just for the starting system. Problem is the hard starting issue and the battery is not charging. Had it wide open on the water with volt meters on the terminals and it only read 12.9 same as when i started. Spoke with the CDI people and they told me to jump purple wire to pos side of battery, however they did not tell me if i should disconnect it first and should i connect directly to the rectifier? The guy said if it now is charging the problem lies in harness or switch.(did not do this test till i am clear on what to do) I pulled the flywheel yesterday and the black coil towards the front of the boat looks cooked, there is signs that black goo dripped out onto the the powerhead. Does that coil assist in the charging system?