Assuming you are talking about RTV silicone. If you are talking about the permatex that uses a brush to apply this is for use with gaskets not a gasket replacement.
I do it all the time. My preference is the red but that really doesn't make a difference here.
Couple of tips to make sure you don't plug up intake screens and have a leak free repair.
1. Make sure everything is clean. Clean the surfaces mechanically then before you apply spray down with aerosol carb cleaner, let that dry (DO NOT WIPE OFF) then apply sealer.
2. When applying the sealer lay out a small bead and smooth with a clean finger. Let it skin over lightly before assembling the parts. You should get small bubbles as you tighten things up. Wait 24 hours before cutting these off and they will come off with a knife easy.
As others have said dis assembly in the future will be hindered if you properly apply.
One important note here though. Is the part you are putting on dependent on the gasket for shaft/bearing clearance. If it is you pretty much better grin and bear the set and go that route.
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