How would I set up the Wendigo's regeneration if only the burning of Wendigo's heart can kill a Wendigo?
That seems easy enough, something like:
Regeneration (Ex): A wendigo heals X hit points per round. The only way to kill a wendigo is to cut out its heart and burn it to ashes. Destroying the heart takes Y points of fire damage. The wendigo does not regenerate on a round its heart takes fire damage.
What if the the creature turned into a Wendigo gains 5d8 if its HD is less then 5?
5 Hit Dice seems a bit low for a Huge monster, 6 or 9 might be better.
It's simpler if the creature keeps its original HD and adds levels of monstrous humanoid on top of that, using an approach similar to an SRD Lycanthrope. e.g.:
Hit Dice and Hit Points: A wendigo adds the Hit Dice and hit points of an X level Monstrous Humanoid to the HD and hp of the base creature.
Base Attack/Grapple: Add the base attack bonus of an X level Monstrous Humanoid (+X) to the base attack bonus of the base creature. Recalculate the grapple modifier based on the wendigo's new base attack bonus, size and strength.
Base Save Bonuses: A wendigo adds the base save bonuses of an X level Monstrous Humanoid (Fort +Y, Reflex +Z, Will +Z) to the base save bonuses of the base creature.
Skills: A wendigo gains skill points equal to (2 + Int modifier) times X from the levels of Monstrous Humanoid it gains. Its Monstrous Humanoid levels have class skills of ????.
How would I go about setting up its disease attack?
If it's a mundane disease like filth fever, it'd be something like:
Disease (Ex): Filth Fever—Bite, Fortitude save (10 + 1/2 Wendigo's HD + wendigo's Con modifier), incubation period 1 day, damage 1d3 Dex and 1d3 Con.
If you want a supernatural wendigo-creating disease, I'd suggest something like.
Disease (Su): Wendigo Hunger—Bite, Fortitude save (10 + 1/2 Wendigo's HD + wendigo's Cha modifier), incubation period 1 day, damage 1d6 Wisdom* and 1d3 Con.
*When damaged, the victim must succeed on another saving throw or 1 point of Wisdom damage is permanent drain instead.
If the victim has their Wisdom reduced to 0 by Wendigo Hunger they transform into a wendigo.
Should its claws since they are two feet long increase its reach with its claws?
No, I wouldn't think they'd increase its reach. Swords can be longer than two feet and they don't have Reach.
Would there be any way I could have the Wendigo able to skate across ice and ski across snow with grace and at triple the Wendigo’s normal running speed?
Sure. I suggest you modify the "Windskating" ability we came up with for the
Scathe.
Windskating (Ex): By balancing on its long foot-claws, a wendigo can skate across smooth, level ice or snow at a speed of 60 ft. [?] If the icy surface slopes downwards it can move 10 ft. faster (70 ft.) on slight grades (less than 30 degrees), 20 ft. faster (80 ft.) on moderate grades (30 to 45 degrees) and 30 ft. faster (90 ft.) on severe grades (45 to 60 degrees). It cannot skate safely on grades of 60 degrees or steeper. The wendigo travels at its normal 30 ft. [?] land speed when moving up icy slopes.
Furthermore, a wendigo can travel faster in the direction of the wind. It can move at a speed 10 ft. faster in a light wind, 20 ft. faster in a moderate wind, 30 ft. faster in a strong wind and 50 ft. faster in a severe or stronger wind.
The speed increases for slope and wind are cumulative, so a wendigo can windskate down a slight grade at 90 ft. with a moderate wind (its base 60 ft. skating speed plus 10 ft. for the slope and 20 ft. for the wind).
How much damage would the Wendigo do with its claws and bite attack?
However much you like! A typical Huge creature has 1d8 damage claws and a 2d6 damage bite, but wendigos have massive claws so I'm thinking you'll want to increase their damage.
Hmm, a Polar Bear is Large and has 1d8 claws. Increasing that to Huge is 2d6 claws - would that do?
Might as well tweak the bite damage up a tad too to, say, 2d8.
Since you can have larger than Huge wendigos, a little damage table would seem in order:
[TABLE="class: right"] [TR] [TD="align: left"]
Size
[/TD] [TD]
Claw
[/TD] [TD]
Bite
[/TD] [/TR] [TR] [TD]Huge[/TD] [TD="align: center"]2d6
[/TD] [TD="align: center"]2d8
[/TD] [/TR] [TR] [TD]Gargantuan[/TD] [TD="align: center"]3d6
[/TD] [TD="align: center"]3d8
[/TD] [/TR] [TR] [TD]Colossal[/TD] [TD="align: center"]4d6
[/TD] [TD="align: center"]4d8
[/TD] [/TR] [/TABLE]