(1) 45:25 "In elections, 'for' and 'against' spaces or boxes may not be used. They are applicable only with respect to votes on motions. In an election, a voter can vote against one candidate only by voting for another who has been nominated or by writing in the name of another candidate." Your Church's ballot with a single line to vote "yes" for a candidate is a bit of a chimera then. It's an election, and so it really should be a box for the candidate and a space for write-ins, under RONR. If it were a motion, you'd need to have a box for Aye and a box for No, which would avoid the ambiguity about whether failing to check the box amounted to a vote against the person or a mere abstention.
"Present and voting" is used in Roberts 1:6 and refers generally to the people voting on the question. People who abstain are not voting on the question.
(2) Not in your case. 46:34 describes a situation where you are electing people to terms of differing lengths, but the ballot does not list those positions separately. In that case, the people with greater majorities win the longer terms. It sounds like you had separate lines for the separate terms.
(3) Sort of a deeper philosophical question, eh? At a certain level, it's the Assembly's meeting, the Assembly's election, and the Assembly's elected positions. You can be quoting RONR chapter and verse but if the meeting is overwhelmingly against you, a ghostly General Robert is not exactly going to ride to your aid.
However, I could foresee it being an issue if some action gets taken that results in legal liability, such that an outside actor (i.e. lawyers, judge) are analyzing whether your organization properly decided to take some action or make some expenditure.
(4) See 2:25 discussing "customs." A custom that conflicts with RONR or other superior procedural rules set by statute or bylaws "falls to the ground" when identified by a Point of Order. A custom that is otherwise consistent with procedural authorities can be suspended by a majority vote.
(5) An amendment to the Bylaws could clarify this practice and 46:30 recommends that organizations adopt specific election procedures appropriate to their organizations. If the Church wants it to be possible to leave an office vacant, the Bylaws should then specify a "Leave vacant" option.