The quality of jumper cables is typically no where near the leads that are supplied with the car or what you can buy as replacement battery leads. One factor is the insulation, for underbonnet use it will be more heat/acid/oil resistant and go the distance without perishing. Also buying the right length leads with the terminations already on them will save a lot of hassle and you can be sure the terminations will be done well.
Alternator, is the pulley from the v6 ecotec and 202 pulley just a straight swap, they are setup for different drive belts, what about the mounting holes for each?
The voltage fluctuation at idle sounds like your regulator/brushes(replacement is about $20-30) is worn, though loose connections are possible.
Depending on your sub, if its high power like 600W, then you are going to be drawing 50A+ on big bass notes. If this is consistently how you use the car(thumping music at idle), then yes you will need more alternator.