Raiden is way easier to play on stick in my opinion...stand 1 vb , d1 dash 1 shocker combos etc in my opinion would be easier on stick than pad, not to mention doing 121, 1212 etc.
Anyways in response to the OP:
a). Where should I be spaced
It's all matchup/situation dependent in my opinion. If you have the life lead use dashblocking and force them to come to you while playing mind games with lightning/superman/tele. B312 is great for whiff punishing combos if the opponent misses while attempting to rush you down.
b). What are good tools for footsies (other than pokes)
B3, B31, F23, F24, D1 VB, Stand 1 VB, D4 are all options for footsies, along with sweep and mixing in throws. It's all about making reads. Also it's a good idea to train yourself to hit confirm the B312 string. For example, you do a B3...if it hits follow up with 12 into a full combo...otherwise you could just go into 1 or stop at B3 then follow up with a throw or other footsies/strings. Also if your opponent likes to jump after you do a D3 (sometimes as a counter to F24), a stand 1 vb combo is guaranteed if they attempt to jump after D3 hits.
c). How to incorporate d4
D4 starts up kind of slow but its pretty effective off of a jump in punch or a follow up for a D3, and after a JIP you choose to either D4 or F4 (overhead). After it hits your guaranteed a block string, but often times it's easy to land a full combo after you D4 (hit), dash 334.
d). What to do for anti-air
D1 dash 1 shocker, en shocker, 1 vb dash shocker, 2 vb dash shocker combos are all anti air options. If you want to play more defensively tele the jump ins and punish or escape jumps/ jump ins with superman. JK followed by a ground superman is a good option as well. If your B312 ends up juggling an opponent follow up with shocker into 33 VB superman or 334/334 tele.