100 series landcruiser roof rack mounts leaking water into car

Dear all, I have just purchased a 105 series landcruiser. I have found that under the vinyl flooring the underlay is soaking wet under the drivers & passenger feet compartment along with the rear boot area. The passesnger section of the back seat was dry. Also in the hollow section of panel in the boot where the tow bar bolts into was about 2cm deep with water.

I've found that the water is coming in the car via the roof rack bolts. They go through the roof channel and bolt to captive nuts up kinda near the handles above the windows.

The set up is this- roof, foot plate of rack, bolt holding the lot down. There seems to be some sort of rubber ring on the bolt but it's very perished and I think water would have run between the roof and rack foot anyway. Be it bad design or old materials I dont know.

My question is, how are your roof racks on 105's sealed up to stop this happening? Does anyone have a suggestion as to how to fix?

My first thought was plumber's thread tape but a plumber I know said that prob wont seal well enough. Second idea was to put a piece of rubber under the foot with a small hole in it to allow the bolt to go through the rubber. The foot will push down and capture it between itself and the roof hopefully sealing it. Not sure if I need a rubber washer for the top of the bolt. The bolt needs to be tight to hold the rack down so it nay squish a rubber washer anyway.

Looking towards your suggestions.