of the parts listings will show you good clear photos of the screws if you click on them, but not all. That can be a real PITA.
Even when they have photos, for some reason the metric
hardware is often shown next to an inch
ruler, which isn't super helpful. I don't know why PartZilla does that.
The parts listings occasionally state the shaft size and length of the fastener, i.e., "Screw 6 x 22" means an M6 screw (6mm nominal shaft dia.), 22mm length.
Screws 1-4 and B are all for securing plastics.
Screw 1 goes in hole #2.
Screw 2 looks like it may be the shoulder screw with a conical head. Those go in the #1 holes, forward and aft of the turn signal, through the shiny black plastic side panel. They are unique on the bike.
Screw 4 goes in hole #4. These are unique to the black plastic panels under the rear half of the fuel tank (Frame Cover in Suzuki parts-speak):
Suzuki 09139-06107 - SCREW | Partzilla.com
B look like they are the big-head screws that go into the lower side cowling, threading into fittings in the radiator sides. But I think you said you already put screw #3 in that place?
The remaining hardware goes elsewhere.
Nut A (whiz/self-locking type, w/flange) I'm stumped by.
There is one on an end of the long bolt at the front of the tank (where you can pivot it up for service once the plastics are off), but I think you stated in your other thread that it is in place already.
Bolt C looks to me like one of those that hold the front master cylinder to the handlebar - #9 here:
Suzuki Motorcycle 2008 OEM Parts Diagram for FRONT MASTER CYLINDER | Partzilla.com
Bolt D: could it be #9 here, since you did stuff with the brakes?
Suzuki Motorcycle 2008 OEM Parts Diagram for REAR CALIPER (DL650AK7/AK8/AK9) | Partzilla.com
As the others said, I would go over everywhere you removed stuff, to make sure no fasteners are missing. You don't need brake system parts moving around that shouldn't, or handlebar controls shifting while you ride.
By now you've learned that some of the hardware was substituted by PO. I can understand why people do this. Many of the fasteners are not available at a local hardware store, or even from a specialty vendor like McMaster-Carr. The shouldered screws for the plastics are particularly exotic.