Yes, he certainly is taking a flow rate hit. I would go as far as to say he might even be gettign HIGHER temps with the second rad, just due to flow rate loss.
The 1250 isn't a bad pump by any stretch, but its definately going to suffer going through two large radiators.
Either one of those rads shoudl be plenty powerful enough to cool your CPU. I am also curious as to why the use of the TEC? (just noticed that in your sig) and just how much wattage (heat) are you dumping into your loop from it?
If you want to quiet yoru machine down, my suggestions woudl be as follows.
Remove on of the Rads from your system (unless you have a specfic need for two, OCd SLI cards possibly?) Dump the TEC, I have a feeling you may be dumping unecessary wattage into your loop and actually causeing higher temps because of it (speculation here based off of "why are you using two rads that large?"). Shroud the rad you wish to use (if it isn't already).
If you can clarify on your loop some more though, that would be very helpful.
EDIT: Ok I see you posted some more while I was typing this up
Sounds like a good plan.