Forgive me, but when I read high res, I expected it would be 96, or 192KHz - 48K is bog standard digital, and pretty normal, so I'm really wondering where your issues are? I think people might be right when they are asking about plugins - and you don't say you are actually using loads of these? Have you tried your laptop as a comparision, with the same files and instrument sources? My main machine is now fairly elderly in processor terms and I simply have no latency problems, have never even changed buffer sizes or other tweaks? I just creat tracks, bring in VSTis and it works. The only real delay is the initial loading time of big sample packages, but once they are in and working - latency is just, well, normal. Maybe you have some kind of computer, rather than music software bottleneck?
When you say lag, you mean an audible delay in things happening, so your timings are all wrong and your mics produce real delays before you hear them - so a clap in the room is a real clap,clap? You are running the latest MOTU drivers? You're sure theyre actually in use and the DAW hasn't secretly swapped them for windows versions? Cubase occasionally switches to ASIO4all drivers when I do something silly, and next boot they are there again?
So - what plugins have you got permanently running, like as in templates, are you, like we are thinking, running bags of them almost automatically, or are you adding them as required?
44.1 to 48 is hardly noticeable in real terms. I've loads of old projects in 44.1 and to be honest, audio wise, I rarely actually notice until something really bright just sounds a little less bright and I notice. With my ears, 96 I cannot hear the difference.