Too warm. Not enough light. Normal home temperatures are quite enough for growing most seedlings unless you can provide strong natural light such as a greenhouse or good artificial lighting. Heat mats can be used to speed up germination but should be taken away afterwards. Certainly they should be turned off at night or your seedlings will stretch like mad. Plants that lean are not getting sufficient light on one side, very common on a window sill. Turn them occasionally so they don't grow completely one-sided, keep them cool enough at night that they grow robustly, and grow them in the brightest window you have. Direct sunlight (or bright lights) is a necessity for most seedlings to grow well.

Yes, it was very difficult the first time I did it and the second time I tried it it was far too much work. So, I actually stopped thinning. Like you, I'll plant two to three seeds per cell and then I take all the seedlings and transplant them into larger cells. I figure it can't hurt to allow the strongest to survive on their own in their own cell. If it dies after transplanting then so be it. That rarely happens and as a result I end up with far more plants than I know what to do with. Last year I think about 60+ plants ended up in the compost pile because I didn't have time to plant them all (way too ambitious in consideration of reality). This year, I'm making room for everything or giving it away ahead of time. Not sure who came up with the concept of thinning but I've decided that's one technique I'll have no part of. :)

Growing seedlings for fruit takes years. And it is best to have them in a deep pot and never trim roots or tops. To get fruit it takes outgrowing the "juv- inile" wood. You may have nice ornamentls growing now but you need to balance mature size with available space in those northern climes. A grafted tree may may be your best bet since they fruit on a smaller size frame.

No room here or I'd be sorely tempted, lol!