That depends, in theory yes, but I was wheeling with a guy last week, that took deep mud, and didn't extend his trans and T case vents, we swaped out the fluid on trail, 2x's and then his trany blew, I think being that your symptoms are improving with each fluid change I think you 03 will make a full recovery!
You said you also extend the Transmission and T case vents???? Then How did the water get in?

98 wrangler 2.5l 3 inch rustys, 2 inch body, 33X12.5 MTR's DETROIT LOCKER, 4.88 gears, moser axles, Dana 44 (rubicon housing)