My searches didn't quite find what I think I need to do.
Here is my situation, I installed Arch linux ARM onto a NAS unit with a USB external drive connected to it. I currently have the OS booting from a 4Gb partition on the drive and the rest is a second primary partition for storage of my media. The Drive is about full and I have purchased a larger drive to use.

Device Boot Start End Blocks Id System
/dev/sda1 * 2048 12658687 6328320 83 Linux
/dev/sda2 12658688 1250263726 618802519+ 83 Linux

The NAS only has one USB port so I would use a PC booted with a live disk and both USB drives connected to copy from one to the other. I've had issues trying to do a similar operation before where it copied the partition to be the same size and then broke when I tried to resize after. I would like a method that will copy the first partition for boot/OS exactly the same, then do the second to fit the rest of the drive while. That way I can easily take the new drive and plug it into the NAS and have it boot right up without having to reconfigure anything.

I'd use dd to start with.
You only need to run it to just after the start of sda2, so it gets the bootloader and all of sda1.
Then delete the (partial) sda2, create a new partition filling the drive, then format & rsync.

Although there's really no reason you can't dd the lot then resize sda2 after.

dd works, but something like clonezilla might be easier for you.

Well I tried to DD the whole drive (took 2 days to complete) but the copy would not boot.

Clonezilla gives errors about not being able to make the partitions and doesn't complete.

Clones don't always work with different hardware. It could be that you need to fix some naming issues.

I am trying to use the copied drive on the same hardware. The copy is on a larger capacity drive, I am trying to make the boot (sda1) partition exactly the same with the second partition filling the rest of the space for storage.

I believe my issue is actually that the new drive does not initialize fast enough for the bootloader on my pogoplug to find it.
old drive was a usb2.0 640Gb seagate and new one is usb 3.0 1tb WD

It is not the same. The cloned hard drive is different by many reasons.

I'd think it unlikely it is not initializing fast enough.

Do you get anything when you try to boot from the new drive?

The reason I believe it to be the drive is I have read others who had issues with certain 3.0 drives with this device, also if I use a powered USB hub between the pogoplug and the drive so the disk is already spinning it will boot.

" if I use a powered USB hub between the pogoplug and the drive so the disk is already spinning it will boot."

Then we can say that it won't work and no way to fix it with this drive without a powered hub. It may be possible that a laptop portable usb drive might work.

It could be that a usb 2x drive might work also or different brand usb 3.