1. The Rupee counter doesn't appear at the bottom left on rooms bigger than the test room that comes with teh engine, but draws itself somwhere down the left side in the middle.
Basically yoshi's rupee engine draws it in that space, so all you have to do is change where it draws it (I assume this'll be in the draw code somewhere).
2. If the room is big enough you can loose the Rupee counter's position all together as it dissappears off the screen.
To fix this, find the draw code and make sure that it's draw relatively to the edge of the room. I'm not sure how yoshi does it, but when you find the bit where you set up the x and y coordinates change the x to something like room_width-40 and the y to like room_height-30.
Now this won't work if you're using views, your gonna have to use the view variables instead. So go check the GM manual.
I cannot answer your third because i don't have the heart engine code, though why exactly it would be yoshi's code that your using to collect rupees I don't know, that's your code probably, so you're gonna need to post it.