Problems using portupgrade to recompile all ports

[Scott I. Remick]

So I'm upgrading my 5.1R desktop to 5.2R. Used cvsup, followed the 
instructions in UPGRADING, did a custom kernel, etc etc. That part went 
fine, no probs.

I noticed some of my daemons (from ports) seemed a bit annoyed though upon 
booting up 5.2. I tried using portupgrade -Rf on them individually, and 
then all was well. I decided then that it'd be best to do everything (-Raf) 
to play it safe. I've done this before.

So it finally finished last night, but not really... about 132 ports were 
failed/skipped. My problem is figuring out the most efficient way to deal 
with it from here. LAST time I did a portupgrade -Raf I had a much smaller 
number failed/skipped, and what I did was work out the dependency tree for 
the remaining ones by hand using pkg_info -R and -r, figure out the order, 
and do a portupgrade -f on each in the proper order. This was to avoid 
rebuilding stuff already built on the first -Raf pass, and multiple times 
over (since I was taking care of each remaining one individually). Seems to 
me that if 50 of those 132 are X apps and I do a portupgrade -Rf on each, 
I'll be rebuilding XFree86 50 times. Hence the need to work out the install 
order by-hand based upon dependencies and only use -f. But I don't see that 
as practical this time around with so many left to do.

So... my ultimate question is: how do you pros handle situations like this? 
Is there a trick I'm missing?