How can I improve this deck ledger and the flashing around my ledger?
Perfect world ... the flashing would be gav metal and create a template (opening) for the vents. Top and side exterior would overlap this flashing top down to DRAIN water (installed as bottom, side, top). I'll mention tar paper here, or peel-n-stick, to underlay and cover any missteps...USE IT.

If...when...you replace the wood, and peel-n-stick the area (bottom up so top overlaps bottom), it will never leak! Your problem is more of a surface issue where the vent is recessed. Fix that and bluff the vent out to make even with the exterior surface, then seal and flash in.

Caulk..and press caulk into any crevises or corners...the outline of the template when finished for a water tight seal.

Don't be scared of the opening, put a hose to it to check for leaks and see where/how you need to repair.