I wish that I could help more but I'm not that familiar with the VPI tables. In my case, I have the scribe line on the manifold just .5 cm above the platter. I think that this might be close enough. I think you should first put the VTA adjustment in the center of its range. Then adjust the attachment of the manifold to the base to put the scribed line even with the platter or close. At that point, if the arm and top of the cartridge are not parallel to the platter, I would raise or lower the manifold attachment to the base. I think that this step is least critical.
You want the arm and cartridge to be parallel to the platter or record surface with some adjustment left on the VTA adjustment. You don't want the adjustment all the way up or down.
If your armboard is wooden, you could add height with a matching piece of stock of suitable thickness. If it's metal, which is better, get a metal piece of suitable thickness cut and attach it with screws.
I'll bet that Bruce has an answer for you. He's pretty quick to answer emails.
These arms can really be a PIA as I said but don't give up on the Lyra cartridge. You can work it out.
Good luck,
John