I would definitely try to get the vacation issue on the table right now...even if they don't budge on this years time, hopefully you can get more for next year, or at least you can get it on paper that you will re-negotiate at the end of the year based upon your performance, etc. Once the employer has you, I feel it is a lot easier for them to say "well, that is our policy"
Explain that you don't have a problem with the 90 day policy, or the limited amount the first year, as you will be learning the job with their company. Personally, I would then see what
they say at that point before suggesting sacrifice of 2% pay, etc.
2 weeks for 5 years with no additional personal days and no roll over is not much time at all...(currently on the 5th year of that deal)