With VSM III and Sim Audio I'd go Cardas Golden Cross throughout, And be done with it. The Ver3 is less fleshed out than the SE, M, MX, or the super easy to listen to "E" versions. The Golden Cross will fill out the mids and lower mids a bit, it has a similar refinement that Sim Audio has too. I would also use the Merlin Jumpers with single wired Golden Cross Speaker cables first. Do you have a Bamm? If not get one ASAP; Fills out the Bottom like a big girl. How bout The Z feet? or do you have the BullDog Cones still? Maybe get a wish list together, a set of Merlin Z Feet, Zobel's, Merlin Jumpers, an older traded in BAMM perhaps, and call the gang at Merlin after the 07 CES. Now I am making a few assumptions here based on your older VSM's, you may well have all the above?(BAMM, Jumpers, Zfeet, Zobels,..)If so, then sweet. Your getting all of your VSM. If not, get those first. As a experienced Merlin owner, they are integral to its design, performance and presentation. Before any other upgrades ANYWHERE else, .....
Back to your original question :), I'd go for the more detailed Golden Cross over the JPS with your Ver.3, and I'd start with the Speaker cables, then the IC between your Preamp/Amp (i Find this IC the most critical in a system), then sources..... The great thing is the Merlin's are so neutral, and faithful to what comes before them, you can really tailer the sound to your tastes (if you know what your tastes are, that is always the hard part - esp if you find yourself in a period of changing aural priorities...)