Ouch. Why waste so many resources getting so many rares to level 40, instead of just taking them to 4* level 1, if you're going to use them as food? I'd keep all of the level 50s and honestly, most of the level 40s have at least some potential use and you already went to the effort of taking them to level 40, so... the uncommon you could use as food, most people only use uncommons or duplicate rares as food anyway. 

Thanks - yeah i sort of played the game without really focussing or working out what I needed to do so just kept levelling!  

In my opinion, it is actually fine what you are doing here as long as you are using these level 40s and 50s for progression. This is what I did during my early game. Level bunch of champions even rank and ascended them to 5 star IF I need to. Then feed them when I don't need them anymore or I have better champion to replace them. So that is instant 6star to me when I get better champion. 

During my early days in this game, it is easy to decide who to feed because there are very limited content you need to worry. No faction wars and no doom tower. These two, make players use non meta champions so any of the champions you have now can have use in these content. 

With that being said, the most typical answer you will get is to 6 star your farmer. And the most commom first 6 star is Kael, since he can be use anywhere in the game.

Keep at least one copy of epic champion, good or not, in case they get buff, you have a copy of it. I will not worry too much on saving a copy of rares since they can be easily summon again and also if you are not spending in the game, storage is very expensive to expand. 

For the rares, you can keep your:

Fellhound 

Painkeeper

Paragon (you can leave him 4star and can be use to clear nightmare campaign and I believe I used him as a tank in Spider 19)

Soulbound Bowyer (I believe she is usable in Spider, I have not build her so I am not sure)

Reliquary Tender (my early game reviver helped me in all dungeon content when I needed a reviver, also her debuff cleanse is very helpful in dragon) 

And of course Apothecary and Frozen Banshee, you probably already know, these are the most use rares in the game. 

If I have your account right now, my choice of 6 stars will be, first Ignatius, I will build him as a farmer for now and also first legendary so I will give love. Next will be Vrask. He is an amazing healer for early game. And surprisingly very helpful in stage 21 of faction wars. And then depending of what I want to focus next, I will probably choose between Frozen Banshee (for clan boss and probably first team for dragon 20) Apothecary if I needed another healer. Reliquary Tender, the one that carry me to stage 20 dungeons

One more thing, these are only my opinion. I don't always do what others do, and I am doing fine in this game. You can do the same. Take these as a guide 😊

Thanks very much for the detailed reply - much appreciated.  I think I've been reluctant to lose any of them really - hence building up so many but realise now I can either keep most (and buy lots of chickens!)  or do need to lose some to progress.