I've recently finished my personal Pathfinder-conversions of the encounters in D0 and D1.5 (for the great Kobold King saga - Merlokrep 4 president XD ! ).
Some conversion were a bit tricky, but I solved them elegantly: the chariot beetle has been turned into a Magical Beast (since it has magical abilities and wouldn't benefit from the mindless Vermin traits anyways), and Pinch-Pinch is currently "just" a normal scorpion (luckily, it has the same amount of HD as a normal companion). And then there's this "Advanced Megaraptor Skeleton"...
First, there are two ways to create the Megaraptor out of a Deinonychus: either improve the HD or add templates. Both are more or less equal, but the skeleton template is one of those templates that are heavily based on HD. Just treating the Megaraptor as an "Advanced Giant Deinonychus" would create a skeleton that's A LOT more powerful than its puny CR would suggest.
To keep it balanced, I'd take the more complex "HD-Improvement" route. But then there's still the other Advanced template. The whole name of this undead creature can be interpreted in 2 ways:
1. (Advanced Megaraptor) Skeleton
2. Advanced (Megaraptor Skeleton)
The first doesn't look quite right. It'll boost the final creature's abilities without influencing the CR. The second even gives a nice HP boost, taking more advantage of the template.
Of course, you could also make a Deinonychus skeleton which is then turned into a twice-Advanced, Giant creature. Sounds rather fair - especially if you want to create a Velociraptor skeleton, which is then treated like a Deinonychus skeleton with the Young template. Otherwise, you'd just make a weak Deinonychus skeleton that has still the same CR as a normal one.
Sadly, I don't really know how to handle the WIS and CHA scores of this creature. Should I ignore the increases from the first Advanced and the Giant template because those theoretically took place before the creature being turned into a skeleton (even though I applied it afterwards for the proper CR value)?
How would you do it?