The most radical modification in the FM MSM kit is the Hydra EMS.
There are several reasons for not keeping the stock ECU:

- There are no known procedures to remap the stock ECU.
- It can't handle bigger injectors properly.
- It has a 6500 rpm rev limit.
- The Hydra eliminates the MAF by using a MAP sensor.
- It has built in boostcontrol and other fancy stuff like a anti lag, configurable inputs/outputs etc.

The Hydra 2.5 box is not specifically made for the MSM but is very adaptable and does all OEM ECU tasks. Its shipped from FM with the latest MSM map and is pretty much driveable without too much setup and configuring.

Here is the box with harness and MAP signal line:

Intalling the hydra was supposed to be a 2 hour job; run the map signal line and ebc wires trough the firewall, put the ECU harness across the center console, throw in the EMS and secure it with the included bracket behind the glove compartment and route the WBO2 cable down trough the center console.
I ended up using one whole evening. The FM installation manual did not give any clues where to run the map signal besides not using a vacum source shared with other stuff. After searching for ages for unused taps in the intake manifoil I tapped the BOV line from the plenum .
There is a suitable hole with a rubber grommet in the bulk head between the fuse box and the ABS unit where the line can be run into the cabin.
It was impossible to get the flexible hose down trough the hole with out getting stuck or going the wrong way.
The trick was to stiffen upp the hose by threading in about 50cm of a wire from a coat hanger and poke the hose down trough the sound deadening material and other obstacles.
I secured the hose in the engine compartment with a wire protector to prevent it from rubbing into anything.

Next up was routing the Hydra harness from the stock ECU plug over the transmission tunnel inside the center console. This turned out to be difficult as the 3 plugs seemed to always get stuck some place in the middle. The solution was to wrap the harness plugs with duct tape to remove sharp edged and make it easyer to slide trough.

The included bracket meant to secure the box did not fit and never will. It must be for fastening the box in a NA or something and was impossible to mount as FM had intended on the MSM:
I used some zip ties in stead and isolated it with foam/polyester to prevent rubbing.
The keyless entry black box had to be relocated to make it fit.
The serail cable goes into the glove box.

The WBO2 cable was routed down to the exhaust via the the gear leaver. I cut a small hole on the right side of the outer shift boot just big enough to get the connector trough. The cable was zip tied to the PPF to prevent it from touching /rubbingthe hot exhaust.

Voila. Everything ready for initial setup and first startup!