Thanks for the link. Based on sheldon's page I checked off everything I've already done.
Pedals: not loose, they actually tightened them when I got there just to make sure.
Crank Fixing bolt: wouldn't know, don't have the tool, never been removed
Stack bolts: have been properly torqued by me every time I remove them to clean the chainrings and the rest of the drivetrain
Bottom Bracket Cups/Retaining Rings Loose: don't have the tool, don't know, never been removed
Pedal Problem: spin fine, nothing wrong with them.
Bent Chainwheel: nope
Front Derailer Hitting Crank: I keep my drivetrain properly adjusted (plus this is more of a knock not a rubbing of the chain or metal on metal hitting)
Saddle Creaky: No, still happens when I mash out of the saddle
Definitely not coming from the handlebars, I can actually feel the knocking when I pedal hard. It also happens when I'm in saddle light grip on handlebars and really pushing it. Also have ridden no-handed on the trainer to check as well.