melody is in the alto part, and it finishes the phrase with a large leap down to G
I would like to harmonise the last bar as a V9 chord
I would like the V9 chord to be in root position as we are at a cadence
Those seem to be the real "requirements" you lay out.
The alto part plus bass required to end on root position would be...
Filling in only three part harmony is one way to flesh out the essentials of (hopefully) complete triads and at least the sevenths of any seventh chords. The last chord really needs the third and unless you want a note cluster in the bass staff, that means it should go to A4, keeping your bass ascent from D3 to Eb3, it seems the soprano should take Bb4 to complete the first chord, then G4 to provide the third on the next chord, which would be...
Starting the tenor on Bb3 seems a more even spacing, and holding that for the second chord puts the doubling on the tonic scale degree to reinforce the tonality, then it seems there is little choice for the third chord. If it's a dominant ninth chord, you should want the chord's seventh somewhere, and the tenor takes it...
The move to the third chord is where all the crossing and leap to dissonance trouble lies. I think you could mitigate that a bit with making the tenor first go up to Eb on the Eb chord, where it's a consonant chord tone, then hold it to be the seventh of the third chord...
...Interesting melodies often have leaps.
This is true, but keep in mind what you are working on: four part chorale style harmony. It isn't an aria or a violin sonata. You don't need to make giant leaps, and a sixth is pretty big, especially downward... additionally to a dissonance. Probably a good basic melodic model to follow with chorale style is that for a cantus firmus which you should be able to find in various species counterpoint books. Walter Piston give a nice rule of thumb in his book Harmony for voice leading, spacing, and leaps: first always move voices by smallest distance (steps or holding tones) then when range, crossing, monotony, etc. issues come up redistribute the voices within a chord. So, if you had bottleneck at a chord like C4 C4 E4 G4, play that chord, then redistribute to something like E3 C4 G4 C5, and then continue. That offers opportunities for more interesting lines (leaps) while avoiding any relative motion concerns. You mostly need only worry about range and doublings.
...trying to break as few rules as possible
I cannot claim to be a master of part writing, but I think I became much better when I focused on the positive models of what to do instead of what not to do. The voice redistribution idea above is a positive to do type. You can reframe most of the prohibitions. Instead of "no parallel fifths" think of it as "similar motion to imperfect consonances." "Prepare dissonances" and "double tonal degrees" are other positives rather than prohibitions.
I think part of the trouble you have with this harmonization example it you loaded up several requirements which seemed to run against the grain of typical voice leading and then got caught up in all the rules being broken by many attempts to move. If you let the music go where it "wants to" - in other words follow the positive norms - instead of forcing it to arbitrary places, it should be easier. Don't mistake that for a straight jacket on creativity. You can still have all dissonance, leaps, and chromaticism. But the point is to look for the opportunities the music presents to do interesting things instead of trying to force them when they don't really fit.
