Your new head is from the higher powered 2.3T, which is a better head design. I am surprised that the valve stems are smaller.

As to the noise, you need to check several areas. The transmission mount may be worn. The front CV joint on the propshaft might be coming loose and in need of repair. The exhaust pipe is now too close to the propshaft and the propshaft is hitting the exhaust while in reverse, check the propshaft for scarring at the exhaust hanger locations.

I wouldn't worry too much about water in the flywheel area. It is somewhat sealed but not impervious to changes in humidity. Remember seeing a light coating of rust? That is normal and nothing will be hurt by it. I think I would have inserted a small diameter hose and sucked out most of the water. The CRC/WD40 won't hurt anything either. On a dry warm day, you could take the car for a ride without the cover plate on the flywheel, letting any vapors escape. But you are heading into the winter/rainy season, so that may have to wait for 6 months.

Have fun down under,

Klaus

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My back feels better when I sit in a Volvo seat