Water leak into passenger foot-well

I have traced the rain water leak into my passenger foot-well, to the seal around the steel cover that the air-con pipes pass through.

The bottom edge of the cover has rusted and a rusty stain is clearly visible in the foot-well under the carpet.

I have tried to scrape flaky bits of rust off the cover but with the pipes etc in the way I'm struggling.

My plan is to press gas tank sealing putty along the joint with the rusty cover and clear silicone around the flange in the foot-well.

Has anyone had this leak before and cured it?

Thanks for the helpful advice throughout the year and a Happy Christmas to you all

Marty (UK) 1999 Boxster 2.5 manual