...You must Clean ALL Contact Surfaces with ACETONE!!
I also use the Ultra Black, on BOTH contact Sides, then as You Did, Let it Just START to 'Tack' then Drop the Manifold. This causes the 'Extra' Silicone To SQUEEZ Into, and Pack, ALL of the Voids, And the (4 Corners)!! Put all 3/8" bolts finger loose. Pull the 4 Studs put in the 5/16 Bolts ,Start Tightening from the Center Out...in 3 Phases, Criss-Crossing. Last Phase Torque to Specs. 5/16' Bolts are less that 3/8' Bolts. A Note! Don't forget the Throttle Cable Bracket goes under the Front/Left Corner, Bolt!
Smooth the Exposed bead with Spit on Your Finger. The Four Stud Alignment was My Invention! I've Never had a Leak, since using Acetone to Clean off Oil!
I Doubt taking out the Bolts Would cause a Leak, Provided You Loosened them One-At-A-Time!! I think You may have had degreaser or slight Oil, on the surfaces. Clean with Alcohol, Maybe.
Acetone Always!
You don't need anti-seize. If you're trying to Seal Oil from the Bolt Holes, use Teflon Tape, or 'Liquid' Permatex, looks like Brown Tar, goes on with the Brush in the Cap. Use Sparingly, You don't want any of this stuff getting into the Oil!
Good Luck With It!
See You on the 'Highway of Broken Dreams'