Something you might want to check that's outside hptuners data, based on what I just went through... Check your fuel pressure with a test gauge on the fuel rail.
My best guess is that my recent fuel pump regulator failed open and my pump wouldn't hold pressure, but I found out it was only a 43 psi pump instead of the 58-60 psi that an LSJ wants. When I discovered this I reinstalled my original pump to troubleshoot (it had a bad fuel level sensor so it wasn't going to stay in) and found the regulator had failed closed... It went right up to 70-80+ psi and kept climbing so I shut it all off.
Point being, there are some misfire reasons that hptuners won't log since the LSJ has no fuel pressure sensor channel unless I just couldn't find it.
With a brand new pump that sits right at 58-60 psi and holds 50-55 psi with the key off, my engine sounds muuuccch better but I think my fuel trims are now off from the data logs I just took and need to retune it some.
It seems pretty common for the LSJ style fuel pump regulator to fail and they are only sold as part of the full fuel pump assembly from what I found.
About the not having many options in hptuners, make sure you're in the 'advanced' view, not 'basic'.