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The pin counts should be the same. The only difference in the connectors that I can think of is that slimline (1.8") drives use a smaller connector. There are three levels of SATA (more if you count the incremental versions). With PCI you are likely to be at SATA 1 which is no big deal speed-wise for a burner.
I'm pretty sure that you know not to buy a PCI-E controller card as that will not work in a PCI slot. It also should not be any big deal to pick up a standard SATA cable and the needed Molex-to-SATA power adapter if I'm understanding your post correctly.
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