So, having moved very quickly from air cooling on my new build to an H100i I had to find a way of installing it correctly in the Antec 1200 V3. I have it installed now and couldn't be happier with it. It's in a push/pull setup with the case fans pushing and the H100i fans pulling.
For those who own or have seen a 1200 case in action may know it's not really H100(i) friendly, however having banished my spindle drives from the system I can now easily mount the rad against the front fans. This has the added benefit of being positioned against the air intakes instead of the outlet fans, making the effective ambient temp the radiator is working with much lower than the air taken from the case.
Importantly there is no longer anything covering the 1st PCI-E x16 slot which was preventing me from running anything in SLI.
For the first week I mounted the radiator against the rear fans, this caused the bottom of the rad to cover the 1st PCI-E slot leaving me with little space. It was also against the left most RAM module which is not good. I though long and hard about what to do, considering taking a Dremel to the case and mounting the rad on the back I decided to try it another way. Pics below before and after.
The mess that was the pre-water loop setup:

Steps to mount this (sorry, not many step by step pics as I was in flow and powering through my build):
- Remove all hard drives from their bays
- Locate boot drive to the top of the case, you can fit 3 devices here so 1 optical and up to 2 hdds. You may be able to pile lots of SSDs out of sight here though if you wish
- Now tackle the 3 x 3 HDD bays. For each one:
- Remove HDD bay and then unpin the fan cables from the HDD housing by bending the metal clasps back (should be obvious how)
- Seperate the drive housing completely from the front fan/grill assembly
- Take the opportunity to vacuum and clean the dust from the fan and filter
- Now I mounted the H100i to the centre fan assembly. To do this I:
- Moved the 2 diagonal screws to the other corners in the fan assembly (you need to do this or the next step may damage the fan control dial)
- Remove the dust filter and top and bottom grill and with the Antec supplied fan securely attached to the assembly drill out the 2 unused fan holes from the front so they’re big enough to fit the H100i supplied “long” screws in the widened holes
- The long screws will now fit far enough through to reach the radiator so you can securely mount it against the middle front fan assembly. Do this by mounting this fan to the top position on the radiator and it will be secure inside the case once put in.
- Now fit the middle fan assembly to the middle position with the H100i attached, using the bottom fan assembly underneath to make sure the spacing is correct.
- Push the air filter back in (due to the screw heads it may take some force and wiggling but it will go back over the screw heads)
- Screw the assembly in with the standard case thumb screws. There are pre drilled holes Antec have kindly put on the assembly with corresponding holes on the chassis. Secure with 2 screws each side
- Now install the top and bottom assemblies with thumb screws in the same way and you’re done with mounting! Now cable tidy, attach block to CPU, finish your build and you’re ready to go.
Removed hard drive housing with H100i mounted to the centre fan (can just about see it inside the case):

H100i from the inside:

Finally neat, tidy and complete (just waiting for a couple of 780 when released):

I hope this can help someone out who's struggling with a similar thing. Comments and questions, as always, are very welcome.
Thanks,
Dan.
Intel 3930K CPU overclocked and stable at 4.6GHZ
Corsair H100i closed loop waterblock for CPU
Asus Rampage IV Extreme motherboard
32GB Corsair Dominator RAM (4 * 8GB @ 1866MHZ, CAS9)
2x GeForce 780 GTX in SLI
Samsung 830 256GB SSD
Samsung 840 Pro 512GB SSD
Antec 1200 V3 case
SilverStone Strider ST1500 1500W PSU
3 x HN274H bmiiid 27" 120HZ 3D Monitors
Synology DS1512+ (5 x 3TB WD Red RAID 6)
Razer Black Widow Ultimate 2013 & Mamba 2012
Sennheiser PC 363D and Razer Tiamat 7.1 Headsets