I have been having trouble with my indy cutting out and have found that the ecu seems to have been getting wet. It has got quite a build up of crud inside it. Does anyone know what would be best to clean it out with? I was thinking electrical contact cleaner but does anyone have a better suggestion?

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Tooth brush and methylated spirits should sort you out

I would take the boards off the metal backing plate, -but not separate the two boards themselves.
wash backing plates in sink
for the boards, make sure they are properly dry. (leave in radiator for 2 days) then brush with soft toothbrush.

proper electrical contact cleaner is meant for this and dries in a few minutes

looks like your ECU is badly located, maybe put it in a container

That is what I thought. Yes it is located in a bad place right under the header tank but there's no extra wire to relocate it and nowhere else to put the header tank so I am going to put it into a container to keep it dry.

Contact cleaner may not dissolve the corrosion, it's certainly not designed to fix heavily corroded PCBs like this. It's worth a try, but it if not then use a toothbrush with warm water mixed with a mild detergent, followed by plenty of flushing with clean water and then use a hairdryer etc. to ensure everything is bone dry. You'll need to have the hair dryer on for 20-30 minutes to make sure there is no moisture left under components.

Putting the ECU inside a container is not a good idea as you will stop any airflow, and some of the components can get fairly warm. Look at extending the wiring loom if there isn't enough slack to relocate it.

[Edited on 31/8/15 by MikeRJ]

I've given it a clean with electrical cleaner which seemed to take the majority of it off let it dry out and the car still runs I haven't been anywhere in it yet that'll have to wait for a drier day. I'm hoping this is going to cure it as it only played up on a damp /wet day, it looks like I'm going to have to relocate it away from the header tank for a start. The stuff on the board looked like dry antifreeze and the board itself doesn't look very bad so fingers crossed it'll be ok.

Freezer bag and some silica gel sachets? Then open it up and give it a good clean? I'd get rid of the moisture as soon as possible...

IIIEEEK! IPA, soak it in it, use a soft brush to get shut of the bits then leave it out to dry off. Then get some conformal coating spray, mask off anything you might want to replace/re-solder in future within reason, and spray the hell out of it with the conformal coating. That will waterproof it as best you're going to get inside the case. I'd then find an IP65 case for the outside but that could be tricky.