Attack transports hold a slightly special significance in my family. My father served on board one of them (the Bollinger, APA-234) during the war, and when I was younger (much younger) I built the old Revell and Renwall kits more times than I can count.
If you take a careful look at photos I think you'll find that, when the ships were painted in wartime colors, the "PA" and the hull number were the same size (i.e., mighty small). Many photos date from the post-1945 period, when the hull numbers were painted much larger (and "shaded" with black). In that scheme the "PA" was indeed smaller. If I were building a model of an attack transport in WWII configuration, I'd make all the letters and numbers the same size unless I had a specific reason to do otherwise.
Gold Medal Models has a decal sheet with small hull numbers on it - but I don't think that sheet contains any letters. If you've got a decent hobby shop within driving distance (in which case you're an extremely lucky person), you might check through its aircraft and railroad decal assortment.
I'll take the liberty of offering one other observation regarding APA color schemes. (I've made this point on the Forum a couple of times already; those who've already read it - stop reading now.) One of the things that stuck in my father's memory was the constant routine of painting the ship. ("If it moves - salute it. If it doesn't move - paint it.") Largely as a means of keeping the hands busy, virtually all the exterior and interior sufaces of the ship were constantly getting scraped, primed, and repainted. Apparently the standard Navy primer during the mid-war years was zinc-based, and a sickly shade of yellow. (As I understand it the peacetime primer was red lead, but wartime lead shortages led to the use of the zinc stuff. I may be wrong about that, though.) The standard drill was to scrape the paint off an area of bulkhead, deck, or whatever (using metal scrapers that made a noise that drove everybody in the vicinity crazy), then apply a coat of primer, let it dry, and apply two coats of the finish color (in the Bollinger's case, haze grey or deck blue. Dad described how "some of our great geniuses" tried to save themselves some time by mixing the grey and the primer together, thereby producing a particularly nauseous shade of green. The chief threw it overboard). The work parties worked on areas that might range in size from a touchup spot the size of a man's hand to several square feet. At any given moment numerous small sections of the ship would be scraped bare, and others, where the primer had just been applied, would be yellow. The only part of the ship that didn't get such treatment was the exterior of the hull itself, which was off-limits when the ship was under way.
One time I built a version of the old Revell kit with "PA-234" on it, mounted it on a nice walnut base, and gave it to Dad for Christmas. That was about thirty years ago, but I still remember the look on his face when he put on his bifocals and saw the tiny spots of yellow, where the primer hadn't yet been covered by the finish coat. I've used that trick on a couple of other models, and it always gets grins of recognition from Navy WWII vets. The key to success is to keep it subtle using a dull, pale yellow in irregular-shaped spots that the observer only sees on really close inspection.
Good luck.