I don't have the instructions you are using but I have used RTV. For an eighth inch gap the bead should be almost a quarter inch high and three eighths wide on the bottom, let it skin over then put the lower manifold straight down without side sliding and torque to spec. The RTV should barely bulge out at the joint. Let it cure for another hour and it should be good to go and last until the next teardown.
A caulking gun with the appropriately sized tube is easiest, but it can be done with the toothpaste style tube, just don't be afraid to wipe it all off and squeeze out a fresh line a couple times, blobs and corrections are not acceptable.
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