With the Phil bottom bracket, you have the luxury of dialing your chainline in to be dead nuts perfect, so you might as well do it. Once you get it all put together the first time, use a dial caliper or fairly precise ruler to measure your chainline at both ends of the chain. If you did everything right and have the right parts, you'll probably be pretty close. Do the math to get the difference between your two measurements and then move the BB sideways by that amount, reassemble, and measure again.

If that DA cog is worn very much, you might as well put a new one on even if you just get another dura ace. DA's cogs are of more than adequate quality for the job; no need for a Phil unless you want to spend the money.

You might consider a gearing change though. I don't know your background, but 48/16 is on the tall side for what I like to ride on the streets where I live. A 17 tooth cog would take you down to a slightly lower gear, about 74 gear inches compared to 79, but then you would have 17 skid patches instead of just one that 48/16 gives you. If you're going to be doing any skidding, you should think about this.