So...

I bought a base layer, Under Armor storm. And I have a wind resistant thermal jacket for riding/running. Wondering what to wear in the middle. When it's truly cold out, plan on wearing my fleece, but when it's only 40 degrees, not sure what I should wear.

Midlayer is the least important layer.
I use layers of wool sweaters, fleece, synthetic padded gillet, polyester or poly-cotton polo-neck, even cotton (the horror!!).
I prefer light to mid-weight layers.
Sleeveless styles are useful additions.
I sometimes put a mid-layer over my windproof for quick/temp insulation.

My mid layer is a Sport Hill jacket. Thin, light and warm. Any adjustments under that are different long sleeve jersey's. Either a thin one or a heavy one.

How about a long sleeve mid-weight cycling jersey? It should breathe well and provide warmth.

When it's above single digits F I usually can get by with just tripling my base layer with short sleeves as the outer most layer. For me it's best to be a little cold at the outset than end up sweating within 15 min. of the ride.

A down sweater works well when it's really cold for warmth; ounce for ounce it's tough to beat down when it comes to insulation. At 40 degrees and above, I usually rely fleece for insulation under a shell that provides some protection for wind.

I sweat a lot so I have collected a variety of different weight merino sweaters that I wear over a light merino base, with a wind resistant shell. I choose the thickness based on the temperature. Works for me from 10 - 40 F, though at 40 I might use a single layer sweater.

Wickng base layer, cycling jersey, fleece cardigan, gortex rain jacket.

My mid-layers have different functions for me and outer-layers can become mid-layers and vice versa
The first function is to bring an easy to reach and light hood that goes under the helmet when i don't want to go for an heavier hood or balaclava. MEC merino T2 hoodie do that well for me.
It also acts as a very breathable single layer after i removed my outer-layer when temperature goes above 60/65F
The third one is to bring a lighter outer-layer with wind protection when i'm too warm and need to remove my outer-layer in colder temperatures. The smartwool PHD Hyfi is my choice.

I'm fond of a fleece shirt I have as a middle layer. I have several base layers to work with some are warmer than others. With that fleece middle layer you just want a warmer base ..? you have also layer base layers, meaning a smooth thin one against your body and a thicker warmer one next then, then your fleece and the wind stop layer to finish it all off. but I think you'd be more comfortable with a warmer base