Starting again is your only real option, these plants will never recover and grow properly.
Auto flowers are crap in my opinion and really need to be grown by experienced growers to achieve decent results. I have been growing for 35+ years and hate them, so not even all experienced growers can see any benefit to growing them over photoperiod plants.
I would suggest growing photoperiod feminised seeds/plants, they are far easier to get great results with and use a lot less electricity to achieve a harvest.
For example - autos need about14 weeks at 18 hours a day of lights on time.
Photoperiod plans need 6 weeks at 18 hours lights on then 8 weeks at only 12 hours lights on.
Do the sums and you will be surprised at how much electricity you can save.
I would also suggest trying some Sweet Seeds seeds, they are ridiculously simple to grow, with exceptional genetics and productive and potent plants. They are my "go to" breeder and my first recommendation for new growers as great results are just so simple to achieve. If you are dead set on growing autos, Sweet Seeds have these too, but honestly, you are far better off with photoperiod fems, their yields and genetic stability is light years in front of stupid auto flowers. Autos are really best for people too stupid to be able to work out how to change a timer. Autos are also no good for outdoor growing, they need 18/6 to grow properly and outdoors is just not enough light for them.
Planting seeds in rockwool cubes is easy peasy and if you are keen to try this method, in my diary "cannabis conundrums" I have posted a tutorial in the germination week that describes this technique. Otherwise planting direct in seed raising mix is simple and my favourite method.
Jiffy pellets should not cause any problems for the roots, but if you used those "biodegradable" cardboard looking pots, they are terrible as they do not break down that easily and often roots cannot escape from them unless they are kept super soggy, and as we all know, super soggy is bad for cannabis. I found this out the hard way when I tried them one year and could not work out why my plants weren't growing. After a few weeks I dug them up and to my horror found completely intact pots with no roots coming out and very stunted plants. Needless to say, I only tried them once!
So, starting again would be my suggestion and trying some Sweet Sseeds feminisedseeds would be my recommendation, the results will astound you and hopefully put you off auto flowers , as you can tell, I am not a fan!o
Hope this helps, ..........
Organoman.