A flashhider and a new scope have made my AR-10 outgrow it's soft carry case. It is nearly five feet long. Looking for a larger case, I am thinking it will look like I'm transporting a body...

If I separated the lower, I think it would fit into a standard two gun case. I realize I'll have to be careful of the bolt carrier sailing away. Besides the possibility of losing the bolt carrier, has anyone ever had issues doing this? Mostly worried about greater vulnerability to damage or reduced accuracy.

Thanks,

No, break it in half if you need too, it's not a delicate little thing, if you used solid components you have nothing to worry about

X2 just make sure you have plenty of room from the edges. I like 4" or more to kinda allow for more protection.

I have to take my stock off my rifle to fit in my bag. I  have 2 LR uppers for one lower, it has no effect on anything.

No you won't. 

With the BCG in battery, close the dust cover before taking off the bottom half.  The carrier won't be going anywhere.  The rifle will be just fine in your case like that.

Gentlemen,

Thank you for the good news.

Off to buy a bag,