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Roman numerals use seven letters: I, V, X, L, C, D and M for 1, 5, 10, 50, 100, 500 and 1,000. Values are added when written in descending order, so XVI is 16. Subtractive notation handles the awkward cases: a smaller value before a larger one is subtracted, so IV is 4 and IX is 9. The system is additive with a subtractive exception, not positional.
The rules on subtraction are narrower than most people assume, which is where errors creep in. Only I, X and C may be subtracted, and only from the next two higher symbols: I from V and X, X from L and C, C from D and M. So 99 is XCIX, not IC — a common mistake. V, L and D are never subtracted and never repeated. No symbol repeats more than three times, so 40 is XL rather than IIII. The system also has no zero and no standard way to write numbers above a few thousand, which is a large part of why positional notation replaced it for calculation.
Because I may only be subtracted from V and X. Ninety-nine is built as XC (90) plus IX (9). Subtraction is restricted to I, X and C, each only from the next two higher symbols.
Purely by convention. Clockmakers have long used IIII for visual balance against the VIII opposite it. Standard notation is IV, and both are widely understood.
No. Three is the maximum in standard notation, which is why 40 is XL rather than IIII. V, L and D are never repeated at all, since two of any of them would simply make the next symbol up.
With a bar above a numeral to multiply it by a thousand, a convention called the vinculum. It was never fully standardised, and the absence of a clean way to write very large numbers or zero is one reason the system was replaced for calculation.