it will be a challenge for sure, to start off with fish known to have ich, but it's a manageable one.
generally speaking as Tony said the bacteria isn't really a huge issue due to the quickness with which you are changing them tank to tank. you can help the process by using an ammonia locker like SeaChem Prime, or AmQuel to help detoxify the ammonia. you can also do water changes to help dilute it in between tank transfers.
TTM is an excellent method. it does require a decent bit of effort, and a lot of water, but it is effective and if done correctly not overly stressful on the animals.
i'm using TTM for the second time right now on a pair of orange spotted filefish, and previously for a copperbanded butterfly. the copperband did very well throughout the process just being transferred, with no additional water changes or ammonia blocker.
the orange spotted filefish are quite a bit more sensitive than the copperband. they're doing very well so far, getting ready for their second transfer tomorrow morning, but since they are so considerably more sensitive, i am using AmQuel and large daily water changes (around 50%) to help keep the water quality as high as possible. they require a lot of small feedings though, so the water tends to foul quickly.
if you were using the method on more hardy fish, like say clownfish, it is a bit easier since they tend to be more tolerant of parameter swings.
things ti watch out for during TTM (and i've learned these the hard way):
salinity. test a couple of times a day since you will need to be manually topping off with fresh water to counteract evaporation.
temperature. make sure your heaters are calibrated correctly ahead of time for the temperature you want, and double check them when you check the salinity.
sharing. it's easy to forget your hands are wet, or your dropper for testing salinity was in the TTM tank, or what have you. be mindful that transferring anything wet is a potential disease transmission vector. so just make sure that if you're doing maintenance on other tanks that you're washing hands, using different equipment, etc...
have as much extra water on hand as possible. the more you have the easier life is, bonus if it's heated, aerated, and ready to go. although i'm aware this may not be practical for many people, depending on how your set up is.
as for other organisms, the choice is yours, and again it depends on your particular setup, and your risk tolerance.
it is entirely possible that an ich cyst could end up on an incoming invertebrate, or piece of macro algae, what have you. so quarantining them is a good idea. TTM even works very well for them. that said, there is probably less of a chance of them being a vector if they are in a dedicated invert system, not in contact with fish. your mileage may vary.
personally i have a second tank set up that acts as a long term observation/grow out system. i usually try to get my inverts in batches and place them in that tank for a while to help mitigate the risk. again, i know this isn't always practical for everyone given space and other constraints.
many people don't qt inverts.
so, different strategies for different people, and i'm sure there are even more techniques. so pick the one that will work the best for you, balancing any constraints you may have in your set up versus the level of risk you're comfortable with.
at any rate, best of luck to you! always good to see people seriously weighing a solid quarantine protocol.
