If I start a war with clan mates that are ineligible due to their eligibility timer not running out, will it skip these members to get the right number of warriors? or do I lose places in the war? Ie. if I have a clan with 42 members, and #30 and #31 are ineligible, will I still get a full 40 member war? or will I have 38?
The system will try to match your clan into the highest bracket based on available members, and remember that clan war team sizes are always in multiples of 5.
When a member is "ineligible for war", they're not considered at all when it comes to matching up for the clan war.
In your example, you have 2 people ineligible and 40 people that are eligible. The system will take these 40 eligible people and start a 40v40 war with 2 spectators. If you had 3 people ineligible thus making it 39 people that are eligible, then it would start a 35v35 war with 8 spectators.