Using a Shimano 105 5800 Crankset with Sora FC-3500 chainset.

Will the chain line be ok?

Personally would upgrade the whole lot unless you need a crank right now.

the only difference between the two will be shift quality ( i have recently made the same switch to full 5800), however this will be reduced due to wrong chain width....basically i wouldn't bother, either replace like for like or upgrtade the whole thing in one go.

If it's just the crank I think you'll be fine. The 5800 is designed for 11 speed (thinner) chains So I wouldn't do it the other way around (11 speed chain on 9 speed chainset).

Reason though? It won't be any better (perhaps ever so marginally stiffer than a new sora crank), but bearing in mind you've got a Sora gruppo you're unlikely to notice.

As per previous poster 10 speed perhaps a worthwhile upgrade for now? I replaced my triple FSA crank to a tiagra 4600 10 speed on my winter bike and it works a treat. The rest of the setup is ultegra (but the old 9 speed 6500series).

If an upgrade is what your after perhaps a whole tiagra 4600 set? About £200ish vs buying a crank separately for £80 - good value by buying the whole group.

Generally, you can mix some combinations of 10spd with 9spd, and some 11spd with 10spd. Mixing 11spd with 9spd, no. The small difference in machining for the outer chain widths etc mount up, and if it works at all it will be bad.

If you're thinking about this as a hedge against a full groupset upgrade in the future, you might be better going for the middle option and find a last generation 5700 10spd crankset.