So I'm guessing I should stop relying on iamnotageek.com's HTJ parse? Where could I find a reliable replacement?
There is NO reliable replacement because HJT is NOT a fixer program, it is to be used for scanning.
Also, it will generally NOT give true readings on a 64bit system. It does work with Windows 7 from what I can find.
We need more information than just
I thought I was noticing some longer than usual load times
Is this longer boot times, longer loads for individual programs, web pages....?

Please follow the steps for scans given in the third link that cauz gave you and post the logs back here.