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He's running a small block. As the OP stated, the bolt holes do go thru into the crankcase. Being it's a 347, most likely he has a Scat or similar stroker crank and they are very high quality with regard to machining tolerances.
That said, teflon tape to "seal" the bolt holes has been an accepted practice on small block Ford engines as long as I can remember and I've been wrenching on them over 25 years. Never had a leak using this method either. That's why it was suggested. A solution based upon real world experience.
With regard to the T5 gears, check for lateral play. MAke sure the throwout bearing snout isn't galled. Hopefully you have the steel input snout, they are a much better piece. Check for brass or dark bits in the T5 fluid (should be ATF for a Ford T5). Shouldn't be any brass or friction material (dark bits) in the ATF. Fluid shoud be a nice cherry red like when fresh out of the bottle. Might want to replace the input shaft seal on the trans while you have it apart. Cheap insurance.
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