Does slow startup time affect system performance?

Just upgraded to a 27" quad-core iMac yesterday and I noticed the startup time is much slower than it should be once I migrated all of my files from my old 24" iMac over. I usually keep my system up for months at a time, so startup time isn't an issue, but the question is: Does a slow startup time indicate that once I'm up and running, the system could be much quicker, too, or is that slow issue solely restricted to just the startup time?

I ask because I'm in debate over whether to spend the better part of a day it would take to do a fresh install and copy my files over from an external HDD, as opposed to the "cloning" I did by connecting a Firewire cable between my old and new iMac to let it do its thing.

Anyone know if my seeing slow startup times means that once I'm logged in, my system could be much faster, or is that slowness solely restricted to starting up?