I made my 1999 contributions into Roth IRA during the summer and have bought and sold stock several times. Now I find out that I
will not be eligible for Roth Treatment because of AGI test...Are there multiple ways of calculating the income earned on excess contributions...are there sources of information..looked at IRS Site..read FOrm 5329 and Publication 590 but can't find answers...

If the contribution was made to an account that has no other Roth money in it, you can choose to recharacterize it to a traditional IRA by moving the entire account at its then current value at the time of the recharacterization.

Otherwise the regs provide only one way to determine how much to withdraw or recharacterize.