No such thing as a 1998 Thunder - the Thunder was a limited run of 2,000 (1,000 in Moondust Silver, 1,000 in Magnum Grey) made in 2001 and the last of the Pumas.
Info on all the special editions available here <--- clicky.
If your seats look like this:
They will have come from a Puma Black edition of which there were 1,600 I think, or a Thunder.
All Puma seats regardless of age are affixed to the floor with 5 bolts - one on each corner and an additional one on the corner closest to the handbrake (referred to from here on in as CCTTH); this is where all your pain comes from I think.
Early floorplan: CCTTH 12mm higher than later floorplan, mounting holes 25mm apart.
Later floorplan: CCTTH 12mm lower than early floorplan, mounting holes 80mm apart (hence needing a top hat riser which raises the floorplan by the appropriate amount and has the holes the correct distance apart).
So your issue is that the subframes on later floorplan seats (like the leather ones) extend 12mm below the floorplan in your early Puma hence why they won't fit. I don't know if it's possible to mount your 'new' seats onto your existing 'old' subframe, or you may be able to find someone who can modify the 'new' subframe for you so it's 12mm shorter in that corner?
It certainly seems like the post-1999 subframe underneath your leather seats is incompatible with your pre-1999 floorplan in any case.