Reclaim hard drive space from deleted partition and reclaim Apple bootloader

Question

I had my system dual-booted with Ubuntu 14.04. However, I found myself not using it enough to warrant the storage space. I deleted the ubuntu partition and the ubuntu swap partition.
However, am now facing two problems that I have struggled to solve.

1. I have been unable to reclaim the disk space from the deleted partitions. I've tried booting into recovery mode Command+R and repairing the disk. The disk repairs successfully, but still remains the same size, and will not let me increase the partition size.

2. The system is still trying to use the grub bootloader. In order to boot to OS X I have to hold down the Option key on startup. This issue is more of an annoyance, but I would love to figure out how to solve it.

Is any of this possible without a fresh install of the OS?

Edit: Screenshot of partition table below. Also, using OSX 10.10.3 Yosemite.

Edit: Could this have anything to do with the Recovery HD below by osx's hard drive on the partition list? Is it safe to remove the recovery hd given that CMD + R reboots are now an online process?

Edit: Output of requested commands below:

diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *320.1 GB   disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS Macintosh HD            245.4 GB   disk0s2
   3:                  Apple_HFS Recovery HD             650.0 MB   disk0s3
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:     Apple_partition_scheme                        *137.4 MB   disk1
   1:        Apple_partition_map                         32.3 KB    disk1s1
   2:                  Apple_HFS VirtualBox              137.4 MB   disk1s2

    sudo gpt -r show /dev/disk0
          start       size  index  contents
              0          1         PMBR
              1          1         Pri GPT header
              2         32         Pri GPT table
             34          6
             40     409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
         409640  479330712      2  GPT part - 48465300-0000-11AA-AA11-00306543ECAC
      479740352     262144
      480002496    1269536      3  GPT part - 48465300-0000-11AA-AA11-00306543ECAC
      481272032  143870383
      625142415         32         Sec GPT table
      625142447          1         Sec GPT header

    sudo fdisk /dev/disk0
    Disk: /dev/disk0    geometry: 38913/255/63 [625142448 sectors]
    Signature: 0xAA55
             Starting       Ending
     #: id  cyl  hd sec -  cyl  hd sec [     start -       size]
    ------------------------------------------------------------------------
     1: EE 1023 254  63 - 1023 254  63 [         1 -  625142447] <Unknown ID>
     2: 00    0   0   0 -    0   0   0 [         0 -          0] unused
     3: 00    0   0   0 -    0   0   0 [         0 -          0] unused
     4: 00    0   0   0 -    0   0   0 [         0 -          0] unused

Answer 1

The disk giving you problems uses the GUID partition table (GPT) to define the its layout. You provided me with the relevant contents of this table when you posted the output from the command sudo gpt -r show /dev/disk0. These values appear to be correct, except for the entry with an index of 3. This entry is shown below.

      480002496    1269536      3  GPT part - 48465300-0000-11AA-AA11-00306543ECAC

The start and size values of 480002496 and 1269536, respectively, are OK, but the contents should be GPT part - 426F6F74-0000-11AA-AA11-00306543ECAC.

To correct the problem you need to boot to OS X Internet Recovery and enter the following commands in a Terminal window.

gpt  -r  show  /dev/disk0
diskutil  unmountDisk  /dev/disk0
gpt  remove  -i  3  /dev/disk0
diskutil  unmountDisk  /dev/disk0
gpt  add  -i  3  -b  480002496  -s  1269536  -t  426F6F74-0000-11AA-AA11-00306543ECAC  /dev/disk0

Once completed, you can boot back to OS X and open the Disk Utility application. The "Recovery HD" partition should no longer appear. You will need to move the slider on the "Macintosh HD" partition as far down as it will go. Click the "Apply" button to recover the free space.

Note: The "Recovery HD" partition has not been deleted. Normally, it is hidden by the Disk Utility application. The partition will still appear when using the diskutil list command. When you move the slider down be aware the Disk Utility application will have to relocate the "Recovery HD" partition to the end of the disk. This can take a while, so be patient after clicking the "Apply" button.

Example Using a Flash Drive

I tested the procedure using a flash drive. Before fixing, the flash drive appeared as such:

Using similar Terminal commands resulted in:

This allowed me to move the slider as such:

Clicking the "Apply" button produced:

In your case, the small free space shown above will not appear. (This is not free space, it is the space taken by the hidden partitions.)