You may get some other opinions on this but here's mine.
These 2.4, PT engines make the most horse power and torque between 4000 and 5000rpm in stock or near stock form. (numbers rounded) After 5000rpm the power starts to drop off quickly. By holding the gear all the way to 6000, you're getting out of the sweet spot where the most power is made.
If you do a search for some dyno test charts or pay for your own dyno, you can learn a lot by studying when the power kicks in. Also note how much the drop is in RPM upon each gear change. Blend these two observations to max your production of power. Try to shift before the power drops off and drop down to where the power is already gotten high.
Another answer to the other part of your question is, yes there can be some loss of power due to plugs and wires. Wider gaps tend to cause missing at high boost. Gapping the plugs down to .042 or even .040 and replacing older, worn wires with high performance wires seems to help. Check around the older posts here and you will find lots of info on cooler air, better grounds, intakes, more boost, etc. Everyone has a little different set-up then the next person but we're all learning from each other.
