Hit Points, Skill points, Saving Throws, and feats need to be selected and allocated carefully. These are slightly more complicated than the attributes because they are quantities that are accumulated or changed based on character level and/or class level. To this end, I've made the assumption that Merlin took twelve levels in Wizard first, followed by nine in Druid.
Unfortunately the second edition description of Merlin did not include any secondary skills or non-weapon proficiencies to work with, so allocation of skills points and feat slots will be purely speculative.
Hit Points: Hit points are determined by class. A wizard's hit die is 1d4, and a Druid's is 1d8. You could roll 12d4 adding 60, (Merlin's constitution bonus (5) per each roll), and then add the sum of 9d8 + 45 and see what comes out. This gives a maximum of 225 hit points, and a minimum of 126.
Armor Class: Merlin's AC in 2E was two, due to bracers that gave him a bonus of 8. This would make his 3E armor class 2.
Saving Throws: When a character has two classes in 3E, his or her saving throws are the higher of he two. In other words:
12th level Wizard: Fortitude:4 Reflex: 4 Will:8.
9th level Druid: Fortitude:6 Reflex: 3 Will: 6.
Thus Merlin's saving throws are Fortitude: 6, Reflex: 4, Will: 8.
Skill points: Skill points are accumulated over time at a number based upon class, so although his total skill points as a Wizard 12/ Druid 9, is 249, they would have been allocated in a specific way. First, allocate the 120 skill points he'd have accumulated by 12th level as a Wizard, taking into account class and cross-class skills. Remember that a 12th level character's skill point maximums for class skills and cross class skills are respectively 15 / 7 (character level +3, halved and rounded down for cross-class).
Next, re-asses what's a class skill and a cross class skill for a druid, and allocate the 129 skill points nine levels in druid would allot. Note, max skill ranks are now 24 / 12.
Feats: Feats accumulation is not based upon class, but character level. All characters start with 1 at first level, and humans are granted a bonus of one extra feat. By twenty-first level, a human character would have a total of nine feats.
Wizards get bonus feats. At first level, they are granted "Scribe Scroll" as a bonus feat, and an additional bonus feat every 5th level (5th, 10th, 15th, etc.) With these factored in, by 12th level, a Human Wizard has "Scribe Scroll, as well as eight other feat slots.
Druids do not gain any bonus feats. By the time Merlin reaches Character Level 21, he would have gained another three feats bringing his total up to "Scribe Scroll" + 11 other feat slots.
Base Attack Bonus: Both Wizard (12) and Druid (9) coincidentally have the same base attack bonuses. Both classes have two attacks per round, the first at a base attack bonus of 6, the second at a base attack bonus of 1.