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Religion is at all times and places a matter between God and individuals...to me, this reads: "A person should be able to decide for himself what God expects of him (one of the more basic Protestant lines

I am in general agreement with your proposition that the Baptists meant, "a person should be able to decide for himself what God expects of him" and I yield to no man a greater respect for your sentiments.

My question to you is this: Why did the Baptists hold that a man should be able to decide for himself what God expects of him; and what are the implications of this principle as regards the authority of the government to attempt to influence a man's religion (namely his prayers and his thanksgiving) by issuing him religious recommendations via executive proclamation?

If prayers and thanksgiving are matters of religion and are at all times and places a matter between God and individuals, then isn't a religious recommendation from the government an intrusion into a matter that at all times and places should be a matter between God and individuals?

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...that no man ought to suffer in name, person, or effects on account of his religious opinions, [and] that the legitimate power of civil government extends no further than to punish the man who works ill to his neighbor." Now to me, this reads...that the civil government (including the judicial branch) should not pass no laws (or make no rulings) that prohibit a person from following his religious convictions [I]with the exception[I/] that those actions should bring harm to a neighbor (for example, the practice of human sacrifice is definately on the "no" list because it breaks other laws, like do not murder).

“...That no man ought to suffer in name, person, or effects on account of his religious opinions” means no disabling of a man's civil rights (to equal protection under the law, to vote, to hold public office, to testify as a witness at trial, to serve as a juror) on account of his religious opinions.

"...The legitimate power of civil government extends no further than to punish the man who works ill to his neighbor" means no civil jurisdiction, authority, power, influence or sway whatsoever over the people’s religion (not even the power to suggest or recommend religious acts such as prayer and thanksgiving via executive proclamation). It also means no civil jurisdiction, authority, power, influence or sway whatsoever over the people’s religious actions. However, actions that work ill to one's neighbor (do injury to another, violate one’s social duties, manifestly threaten the existence of the state or constitute overt acts against peace and good order) will not be excused merely because one commits said acts under the color of his religion.

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The Baptists then complain that, even though they are currently recieving an acceptable level of religious tolerance (no one is declaring that we shall all be Methodists), this freedom they "enjoy as favors granted, not as inalienable rights." They also have to put up with "degrading acknowledgements," etc.

What were the "degrading acknowledgements?"

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"It is not to be wondered at therefore, if those who seek after power and gain, under the pretense of government and Religion, should reproach their fellow men, [or] should reproach their Chief Magistrate, as an enemy of religion, law, and good order, because he will not, dares not, assume the prerogative of Jehovah and make laws to govern the Kingdom of Christ."

What were the prerogative of Jehovah that Jefferson did not dare assume; and what laws to govern the Kingdom of Christ did Jefferson dare not make?

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"It is not to be wondered at therefore, if those who seek after power and gain, under the pretense of government and Religion

"Those who seek after power and gain, under the pretense of government and Religion" were those politicians, ministers and Federalist newspapers that criticised President Thomas Jefferson for not issuing religious recommendations via executive proclamation as had been done by Presidents Washington and Adams. The Federalists attempted to pressure President Jefferson to issue a religious recommendation via proclamation upon the occasion of the 1801 ceasefire and commencment of negotiations that resulted from Lord Nelson's victory at the Battle of Copenhagen on April 2, 1801. (The Baptists wrote to Jefferson in October of 1801)

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My purpose in posting his address was in relation to the other matters we have been discussing, such as whether Washington understood the purpose of the 1st ammendment

When Washington delivered his inagural address, the proposal of amendments that eventually became the Bill of Rights had not even been brought in the House by James Madison.