Lots of questions there
To be absolutely honest with you, I have never had this in any of my tanks so I have no experience in treating it myself. I will try to help but I think you would be better off researching everything a bit more off the internet.
Well first off, I asked about the snail because a lot of treatments can't be used on them and also because they too can ahrbour the parasite and, as a result of these two things, could easily start the whole thing all over again.
Sorry I can't be of much help when it comes to the fluke treatment. I'm not familiar with the particular brand so I don't know what's in it. IMO though, you should try to get hold of a medicine made especialy for anchor worms. You should be able to order it online if you are prepaired to do so. I would have hoped that an LFS in your area would stock appropriate treatments but, obviously, it's up to you to search around and see if they do.
What you did sounds about right and, hopefuly, it should work. However, you will need to do daily water changes (replacing the meds each time) in order to keep water quality up. As the bowls are not cycled (and will not cycle duing the course of the treatment either), 100% changes may be necessary. To be honest, I would be weary of putting 3 fish to a gallon bowl. Water quality will deteriorate ridiculously fast and the water changes are going to be stressful.
If it were me, I would have treated them in the 40 gallon and waited for all signs of worms to dissapear. Then I'd keep the treatment up for a couple of extra weeks and, at the first sign of the parasite returning, would resume treatment for a logner period. Removing the worms first was probably a good idea but - how did you do this? Many of the 'conventional' methods don't actualy kill the worm - they remove the 'tail end' if you like but the head is left embeded in the fish and survives. I'm not sure whether this at least stops them reproducing.
I do see why you are going for the bowls but, unless you are fully aware of the risks, even putting all the fish in the 10 gallon may be a better option than having them in the little bowls. If, of course, you feel confident doing what you are, by all means continue.
I don't know exactly how long you need to keep the fish in the bowls. There should be instructions with the med. It varies from one to the next. If you need to treat for a long time, add an aerator to the bowls. Make sure you watch all the fish carefuly. At the first sign of distress, do a very large water change with fresh water and let them recover before continuing with the treatment.
You asked how you do water changes in bowls - well I feel you need to do full water changes which will involve catching the fish and moving it to a seperate container each time. This is going to be stressful for them so make it as quick as possible and lets hope you don't need to keep them in the bowls too long. What I would do is fill up a bucket with fresh, de-chlorinated water and add the appropriate amount of each med/salt etc to it. Then catch the fish from their bowl and put them in the bucket. Empty the bucket and rinse it out. Re-fill with water from the bucket using a syphon or airline tubing and return the fish as the bowl fills. Any extra water left in the bucket you should throw away and rinse out the bucket with hot water. Then repeat for each bowl. You could do 90% water changes and elliminate the need to move the fish around but, to be honest, it probably wouldn't be enough to maintain good quality water.
If you are prepaired to cycle both tanks again and to strip them down and clean everything up etc (keep in mind this will eman the fish are stuck in the bowls for longer though), I suggest you take everything apart. The tank, gravel, ornaments, filter, heater etc will need to be rinsed in water seperately, where appropriate, hot water is better (watch as some things may be damaged - such as the tank itself - by hot water). Whatever you can, soak in a mild bleach solution. Then RINSE. Finaly, let everything dry thoroughly in the sun. Keep in mind that you are going to need to get new filter media.
When the tank has been set up again (I suggest you let it all dry outside in the sun for at least a day or two, then rinse out one last time to get rid of any dust that has settled); do a fishless cycle. This is much faster than cycling with fish so you'll be able to put the inhabitants in quicker and you'll be able to put them all in at once.
Ok, something I think you should do - strip down the 40 gallon only. Keep the 10 gallon cycled by throwing in a little fish food every 3-4 days (you'll have plenty of time after you've cycled the 40 and all the fish are ok to take the 10 apart as well and repeat the whole process). Just a tiny bit. It will rot and produce ammonia to feed the good bacteria. Then, if you've decided you are up to it, start taking apart the 40 gallon right away. Set it up again afterwards and start the fishless cycle (link in my signature about this if you don't know how it works). That'll save time so that when the fish' treatment is over they will need to spend less time in the bowls. The reason I'm telling you to keep the 10 set up and cycled is incase 'plan A' doesn't work out. I would also treat the 10 gallon as if it had fish in it - ie, add the appropriate meds and do a weekly water change to keep nitrAtes low. Raising the temperature may help. Right into the 80s (deg. F) should be fine. Just remember that, in the event that you do need to use this tank after all, you lower the temperature first! If you see your fish are not doing well in their bowls, don't hesitate to make use of the 10 gallon.
I'm sorry I couldn't realy be of much assistance with the medication and treatment. Like I said, I've had no experience with this parasite myself. I think you should probably try to find one that targets anchor worms in particular and follow the instructions given with it. That would be the safest thing to do. What you are doing now sounds ok but risky and I'm not sure whether the fluke treatment will work for the anchor worms effectively. How long it will take I cannot say. This depends mostly on the medication(s) you are using realy.
If someone on this forum has treated for anchor worms before, please do add your input!