Guitar rig help...

This will help you understand and safely mitigate any ground loop issues. I ran into ground loop hokeys when I gigged with an A/B/Y two amp rig years and years ago.

Multi-Amp Rigs 101 from Seymour Duncan's tech section

Other than that ... 99 percent of the time, your wah and your TS-9 are going to sound better in front the amp versus in the effects loop, which are typically best suited (or sounding) for modulation effects. I'd go wah > TS-9 > amp input. Delay in loop. But your own ears are the litmus test - do what sounds best to you. Case in point: A rotary/Leslie sim is a modulation effect, but I like them better in front of an amp versus in the loop. I'm the same way with phaser pedals in general. Go figure.

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A rotary/Leslie sim is a modulation effect, but I like them better in front of an amp versus in the loop. I'm the same way with phaser pedals in general. Go figure.

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I think this is a result of some pedals sounding better being "pushed" by the guitar sound and get lost or mushy when looped. I'm pretty much with you, although I don't use a lot of effects. FWIW, if you can get past the processed sound, a lot of the digital effect emulators do a decent job of cleaning that up, relatively speaking, and they let you assign the effects in various orders. Even if you didn't gig or record with them, they probably have some value to help you align your actual effects to best outcome without spending hours patching/repatching, etc.