I have placed the shims both ways. That is horseshoe shape rubber on inside or on out side. Horseshoe inside, than wear indicator will fit on inside. Which 9 out of 10 times I find inner pads wear faster. So I like wear indicator on inside. It's also where I find them, most times. I sometime put inside top, as top clips seem to stay a little cleaner. But FSM shows wear indicator (outside bottom) positioned. Which means horseshoe out side.
But having horseshoe shape rubber of squeal shim inside pad. This may give just a little delay in braking. As piston must pressing against shim must take-up the void between shim lacking rubber back at that point, until contact with back of pad. Will driver notice, not likely. Will braking be affected, doesn't seem to.
Fitting clips (pad support plates), I remember it as Top Side In, Bottom Out. Does it matter, likely not. I just make sure tabs do not hit boots. But it is they way FSM appears to show, and how I see them the most in lowest mile 100 series I work on.
Here pictures of a 64K miles 100 series rears fitting clips (pad support plate).
Notice FSM show 2 different grease used. I use the two Toyota recommended grease as shown. Toyota Rubber grease (Lithium soap base glycol grease) is a very light watery grease safe on rubber. Disc brake grease, is thicker and has additives (possibly moly or graphite).
Also notice; FSM show lower sliding pin and rubber bushing as non-reusable. IMHO I believe this is if rubber bushing separated from pin. But if I find any wear on either pin or bushing. I replace the new OEM lower pin w/bushing assy.
FSM also shows the pin boots as non-reusable. These are a very good part to not only replace during servicing. But to inspect annually. If they're not in proper working condition, seated properly and tight. We get water entry into pin bore of torque plate. Which will damage the torque plate. If pin bore of torque plate enlarged, pins move excessively. We may get some brake clunk. We may also get some vibration while braking.
Also be aware, calipers have and R (right side) or L (left side), molded on them. As they are side specific. Torque plates are not. But note, pin w/bushing goes on bottom.