Sounds like they were probably root bound and stunted from not having enough room or nutrients to grow. They should have been potted up at some point. You were doing fine until the 3 months in a tiny tray...

When you're not ready to plant out, you can always put them in larger pots.

My April starts all got potted up at least once before I transplanted them.

How is your soil? Lots of compost? Fertilizer?

I would dig up one of them and examine the root ball. If it is still tightly bound up break it lose some as is usually done with transplants and replant it a bit deeper so new roots can develop along the buried stem. Remove any blooms on it and wait a week see if it doesn't kick into new growth. If it does repeat the process with the others.

nothing to lose and possibly something to gain.

Dave