I don't know the Intrepid at all, but a common source of small focus errors is the ground glass being inserted facing the wrong way. It's normally with the ground side facing towards the lens, and if there is a Fresnel sheet, and the glass holder was designed to hold a Fresnel sheet, the sheet goes on the lens side of the ground glass with the inscribed side facing the ground glass. If the glass holder was not designed to hold a Fresnel sheet, then the Fresnel goes between the user and the ground glass with the inscribed side against the ground glass.
I shoot close-up portraits in 4x5 regularly. I shoot at F16 or F22, I have tried shooting at apertures wider than that and personally, I think you just get too many missed shots. On top of that, it is very tough on your sitter. I would also recommend putting your sitter on a tall stool, that made a massive difference for me, it cuts down hugely on wasted shots.
I don't think f/64 on a large format lens would be considered "extreme". As jnanian explained somewhere (I can't remember) it's not the f/number but the actual size of the aperture opening...I think. So, since f/64 on a large format lens is probably a larger opening than f/22 on a 35mm format lens, there is little chance of diffraction. I just measured my 50mm Jupiter-8 lens - f/22 is about 2mm in diameter. On my Fuji 180mm - f/64 is about 3mm.