Is it possible to only utilise SMBus on PCI Express 1X?
SMCLK and SMDAT are the SMB clock and data connections.

TCK, TDI, TMS, TRST and TDO are the JTAG connections.

The PRSNT1 and PRSNT2 pins are there to tell the host (motherboard hardware and operating system) how many lanes of the PCIe you are going to be using. Since you don't actually intend to use the high-speed lanes at all, I doubt that they're going to be relevant. There aren't going to be any pre-existing drivers for what you're doing, so "registering" the board won't be terribly meaningful. But it would probably be OK to short them anyway, just to let the system know that the board is there.