Let me add my 2 cents and give you some info to before you start.
Stop Watch: These appears after you pull up 4 big veggies. The next big veggie you pull up is replaced by the Stop Watch itself.
Small Heart: These appear after defeating 5 enemies.
Starman: These appear after collecting 5 cherries.
What I was thinking for this would be to go ahead and replace the cherries with regular Mario Bros style coins as initially planned.
100 coins for an extra life as normal, too. However, there is the issue of there being far less cherries in a stage than there are coins in a normal mario level.
To that end I'd consider maybe having alternative ways of gaining coins like in some of the other games.
One idea is that defeating an enemy could spawn a ground coin similarly to SMW. This may require that the sub-world coins be replaced, but that might work out for the better anyway. Especially considering that the bonus game can often and fairly easily be an over abundant source of extra lives.
As for the placement of stars, having them replace the stopwatch altogether would probably be a great choice. The space taken up by the stopwatch and it's effect could be cannibalized for the new enemy spawned coins, too.
Next is the bonus game coins (or veggie coins for short). I think these should affect your 100 coin count. With the inclusion of cherries, veggie coins, and the new enemy defeated coins then the abundance of coins is much closer to what would be normal for Mario 1 & Mario 3. As for the bonus game chances themselves, I find it annoying to have too many chances at the game. It can take a long time to get through when I really just want to get on with playing the main game. So I propose that we do indeed have red coins, but very much like in other games that have these bonus coins. So, let's say when you convert the cherries into regular coins you have a bit of code that allows you to have a red type based on some factor; perhaps a look up table if there is space for it. Then 5 of the cherry coins in each level can be a hidden red coin. Now collecting each red coin will give, say, 2 chances at the bonus game for a total of 10 chances per level. This will limit the amount of time spent on the bonus game and prevent an over saturation of available extra lives. If need be the rewards for the bonus game could be increased if having a max of 10 chances per stages reduces the number of extra lives too much.
To sum up:
100 coins for an extra life.
All cherries converted into coins
Veggie coins add to cherry count
Defeating an enemy grants a coin.
1 red coin for 2 bonus game chances.
Red coins are hidden among cherry coins, 5 max per level.
Stopwatch replaced with Starman.
5 defeated enemies for a small heart.
And one last thing I would request is changing the 1up mushroom's graphics so that it doesn't literally say 1up and has a green palette like a proper 1up mushroom should.
If you ever want to try to overhaul the power up system I would totally support this too. I guess the issue with that would be how to get them without having question mark blocks. The obvious choice is to have them be new items that can be plucked from grasses. I dunno, another subject for another day.