You're prolly gonna be too busy with other issues but when you have time...
You know I'm always open for new ideas to be safe. I always rinse the vails, stoppers and glass with IPA91 for roughly 10 min or so. il start using 70 now due to the rubber you say. Never had any issues though.
Anyhow, then I rinse with distilled water because I don't trust the tap water. Then throughly wash all glass, stoppers and caps with Dawn. Again rinse with distilled water and I don't let them sit to dry. I put the glass in the heat for roughly 3hrs @ 450*. Stoppers and caps 15min @ 170*. When I remove them, both are covered to avoid air contaminants(as much as possible).
I've never had any visible residue, water spots or floaters of any kind. Out of 90 plus bottles never had a Infection or redness of any kind either. (Knock on wood).
When a serious topic comes up, the bullshit takes a back seat so no, I won't be to busy to answer this my friend.
I'm not saying you're wrong bc none of us can ever match pharmaceutical standards in regards to sterility. This post is strictly my interpretation of how we can best mimick those standards with what we have commonly available to us and what will keep us the safest. It doesn't mean I'm right or wrong, simply my opinions to which we can all have a positive discourse on.
The big things I notice in your process that I really like are that you don't wait for the stoppers to air dry in the open, you place them in something covered to protect from contamination, and you use dry heat depyrogenation for glass ware. These are some key things I like to see anyone do.
This is what I would do personally:
For glass ware, I first wash them out and clean them. I obviously reuse all my beakers, my glass media jars for bottle top filters but I also reuse my 20ml and 100ml vials (cleanimg them out of all the oil can be a sumbitch at times lol. To wash them I use cascade pouches of detergent used for dishwashers. I dissolve them in hot water and agitate the water so it gets mixed with the detergent. You can also use Alconox (specifically made for lab glass) as well. For stubborn fat residue you can even use a sodium bicarbonate (baking soda) solution with with water and it should make breaking down the fat easier. If you want to continue using soap I guess it's fine just make especially sure to rinse well so as not to leave residue behind (I'll go over a good rinse procedure). I have a special brush to use on them also for the stuck on stains in the beakers and the vials. Just make sure it's not too abrasive of a brush. Let glass soak for a while to loosen up the "contamination" and mix them around in the water. At this point rinse everything off well several times with regular tap water if you like or distilled water. If you use distilled water here throw it out after. The next rinse we do though you can reuse the distilled water but not the distilled water from this step.
Now let them soak in 70% IPA for 15-20min. Agitate them again every few minutes to get everything moving. Now we rinse again and this is the important rinse. You can use tap water here again at first. Open the tap water and rinse the glassware and vials. Fill them up with tap water and keep the water on to let the water overflow for a short period of time. Then you fill them up around half way with more tap water, cover the only up your hand or finger and shake vigorously and empty. You do this half fill, shake, and empty with tap water a minimum of six times (especially if using soap). After this you make a bath of distilled water and use it to submerge and rinse the glass and vials 12 times. Even though the distilled water from this final bath can be recycled, You can see why you might want to use tap water for the other rinses...you'll run through a shit load of water to rinse everything properly.
Now at this point you can either autoclave them with a pressure cooker for 1hr or depyrogenate with dry heat in the over for ~1.5hrs at 450-500deg. One of these steps are crucial bc if there are any viruses or spore containing bacteria, this is what will kill them. If you use a pressure cooker you want to place something inside it so the glass rests on this stand and doesn't sit in the water, this is crucial for it to work right bc it's the steam that sterilizes and not the hot water. If part of the glass is submerged in water then it won't be exposed to the steam and thus won't sterilize properly. After this you can dry them off in the oven so as not to let them dry in the air and leave them exposed for long. If you go with dry heat sterilization, I get a clean oven tray (metal or Pyrex) and place everything on it. Put a small extra tray in the oven and layer the bottom with aluminum foil; I'll get to why later. Turn oven on 450-500deg F and make sure to preheat the oven. If you out your glass in there before its preheated then don't start timing until it's preheated. 450-500deg F for around 1-1.5hrs is plenty. You like to use 3hrs and that's fine. Absolutely nothing bad will come of 3hrs except a slightly higher electric bill so do whatever you like.
For rubber stoppers, soak them in 70% IPA for 15min or so. It's absolutely best to pressure cook these. Again, if you do it, make sure the stoppers are on some sort of stand and not submerged in the water. I like dry heat for the glass bc I can't fit everything into the pressure cooker but I do use pressure cooker for the stoppers. If you skip this step you run a much higher risk of getting infection. Not saying you will def get one but pressure cookers are cheap downy take the risk? After pressure cooking for 1hr, lower temp in the oven to around 180-200deg (your 170 is fine too). Place the stoppers on the extra tray with aluminum foil and dry the stoppers out quickly.