no - DON'T FIRE .30-06 AMMO IN YOUR 35 WHELEN. Get a set of 35 Whelen dies like from RCBS. That is the brand I used and it has a tapered expander.
Lube your new or once fired '06 brass (older brass may be too brittle at the mouth) and run it into the die to size/decap.
Clean cases and reprime. For a fire forming load, use the lightest load listed for the powder you select. Don't worry about accuracy. And do not use a load lighter than listed as this may also give you pressure problems. Thes light loads will be more than suffucient to form the case shoulder to the chamber of your Whelen.
I believe you can also buy 35 whelen brass from places like MidwayUSA.com or Midsouthshooterssupply.com