Cloned partion to new drive - IO Wait crushes server

Question

I am running Ubuntu 9.10 and recently needed to upgrade the HD. I bought a 3TB 7200 64mb cache replacement drive. Created two partitions one at around 2gb the other for the remainder. The machine is running 64bit and has 24gb of ram in it.

Using clonezilla i copied the / partition from the old drive to the new drive with the larger partition. Everything seemed to have gone fine. But know when we run anything the system just gets crushed on HD activity and the server utilization goes crazy but its all in io wait.

hdparm /dev/sda && hdparm -i /dev/sda && hdparm -Tt /dev/sda

/dev/sda:
 multcount     =  0 (off)
 IO_support    =  1 (32-bit)
 readonly      =  0 (off)
 readahead     = 256 (on)
 geometry      = 364801/255/63, sectors = 5860533168, start = 0

/dev/sda:

 Model=ST3000DM001-1CH166, FwRev=CC24, SerialNo=W1F24V4R
 Config={ HardSect NotMFM HdSw>15uSec Fixed DTR>10Mbs RotSpdTol>.5% }
 RawCHS=16383/16/63, TrkSize=0, SectSize=0, ECCbytes=4
 BuffType=unknown, BuffSize=0kB, MaxMultSect=16, MultSect=off
 CurCHS=16383/16/63, CurSects=16514064, LBA=yes, LBAsects=5860533168
 IORDY=on/off, tPIO={min:120,w/IORDY:120}, tDMA={min:120,rec:120}
 PIO modes:  pio0 pio1 pio2 pio3 pio4
 DMA modes:  mdma0 mdma1 mdma2
 UDMA modes: udma0 udma1 udma2 udma3 udma4 udma5 *udma6
 AdvancedPM=yes: unknown setting WriteCache=enabled
 Drive conforms to: unknown:  ATA/ATAPI-4,5,6,7

 * signifies the current active mode


/dev/sda:
 Timing cached reads:   4596 MB in  2.00 seconds = 2299.01 MB/sec
 Timing buffered disk reads:  458 MB in  3.00 seconds = 152.58 MB/sec

free
             total       used       free     shared    buffers     cached
Mem:      24741804   12299584   12442220          0     244108   10698324
-/+ buffers/cache:    1357152   23384652
Swap:     10490436          0   10490436

Now i will run something something that before the HD change didn't cause barely any issues. Before launching the process system was at about 40% utilization. After launching it and after just a few minutes of it running its at 500% utilization.

Cpu0  :  0.0%us,  0.2%sy,  0.0%ni, 24.3%id, 75.4%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu1  :  0.3%us,  0.0%sy,  0.0%ni, 80.9%id, 18.8%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu2  :  0.0%us,  0.3%sy,  0.0%ni, 16.5%id, 83.2%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu3  :  0.0%us,  0.5%sy,  0.0%ni, 24.2%id, 74.9%wa,  0.0%hi,  0.5%si,  0.0%st
Cpu4  :  0.0%us,  0.0%sy,  0.0%ni, 52.6%id, 47.4%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu5  :  0.0%us,  0.7%sy,  0.0%ni, 51.3%id, 48.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu6  :  0.3%us,  0.7%sy,  0.0%ni, 84.0%id, 15.0%wa,  0.0%hi,  0.0%si,  0.0%st
Cpu7  :  0.0%us,  0.0%sy,  0.0%ni, 81.9%id, 18.1%wa,  0.0%hi,  0.0%si,  0.0%st

I was unable to run hdparm -Tt command because it got stuck waiting.

Here is my fstab and fdisk just because....

# /etc/fstab: static file system information.
#
# Use 'vol_id --uuid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass> proc            /proc           proc    defaults        0       0
# / was on /dev/sda1 during installation UUID=f82c7af2-a461-4d21-ab46-cb579a8a7142 /               ext3    relatime,errors=remount-ro 0       1
# swap was on /dev/sda5 during installation
#UUID=c1c9c112-44e2-41cb-aaae-469f95d0ab46 none            swap    sw              0       0 UUID=3f4ae381-4335-4cc8-a553-842281c57943 none            swap    sw              0       0 /dev/scd0       /media/cdrom0   udf,iso9660 user,noauto,exec,utf8 0       0
#//10.0.2.1/incoming /mnt/pickpackship cifs uid=1001,gid=1001,auto,username=samba,password=Ta2|1TtG3^1 0 0

Here is fdisk and parted info just because...

fdisk -l && parted -l

WARNING: The size of this disk is 3.0 TB (3000592982016 bytes).
DOS partition table format can not be used on drives for volumes
larger than (2199023255040 bytes) for 512-byte sectors. Use parted(1) and GUID
partition table format (GPT).


Disk /dev/sda: 3000.6 GB, 3000592982016 bytes
255 heads, 63 sectors/track, 364801 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Disk identifier: 0x000842cc

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1      254557  2044729071   83  Linux
/dev/sda2          254558      255863    10490445   83  Linux
Model: ATA ST3000DM001-1CH1 (scsi)
Disk /dev/sda: 3001GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Number  Start   End     Size    Type     File system     Flags
 1      32.3kB  2094GB  2094GB  primary  ext3
 2      2094GB  2105GB  10.7GB  primary  linux-swap(v1)

HELP