Differences between expressions including [not/no + more/less + than~]

Examples #1 and #2 are identical semantically. #2 is the more common way to express this. They both equate to your rephrasing #1.

Examples #3 and #4 are identical semantically. #4 is the more common way to express this. They both equate to your rephrasing #3.

As for your rephrasings 2 and 4:

• I have only 1000 yen This means that I have 1000 yen, but I wish I had more. So indeed this is a negative sense.

• I have as much as 1000 yen This sounds as if perhaps you have something else other than yen (dollars, perhaps; or gold) which you judge to be worth 1000 yen. It is "as much as" (equivalent to) 1000 yen. This is neutral.

You could say, for example, "I might make as much as 1000 yen for this [task]." This means you hope to make that much, but might make less (or maybe a little more).

If you were to say "I can make up to 1000 yen", it is similar to above, but it is not possible that you will make any more than 1000 yen.