Measure the ideal bolt lengths for each location and go shopping. If you can’t find the exact length bolt you need for some then buy longer ones and cut them down, carefully chamfering and deburring the cut ends.
Forget about using studs.
Your issue is not uncommon, i had to go through exactly what I described when putting a new set of RARE 1967 GTO manifolds on one of my cars. The hardware they sent was poorly chosen.
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1964 Tempest Coupe LS3/4L70E/3.42
1964 Le Mans Convertible 421 HO/TH350/2.56
2002 WS6 Convertible LS1/4L60E/3.23
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