I've run the Man-A-Fre 6 to 1 header since I bought my truck back in 2000. I had the exhaust system redone in 2003 or 2004 and it matched up to the header.
The first header developed a crack a few years ago so I bought another Man-A-Fre header. It bolted right into place.
Sure the floor under the drivers side gets a bit warm, but I've never really seen this as an issue. The Land Cruiser is cold in the winter and hot in the summer, just the nature of the beast. Cold starts haven't really been a problem for me when I was DDing my FJ40 in the winter.
The 1 vacuum line I have (the vac advance line from the carb to the distributor) is a high temp silicone line, so heat embrittlement hasnt' been an issue.
If you've got a good stock exhaust manifold and downpipe, keep running it, if you don't, go for the header. Just my humble opinion.