Well 'Zelda Hourglass' works for me OK with no problems - got through the intro, got pass the creating save file & as far as actually controlling Link
I'm using the same WoodR4 version with a 8Gb class 2 MicroSD card on a DSLite BTW ....
Did you format your MSD card before installing everything ???
Did you already have a sav file on your card or did you allow it to create a new one ??
As for the 'trimming' - all that does is remove some excess 'garbage' @ the end of the ROM code to 'shrink' it smaller - it won't fix problems (in fact IF you try using it on a DSi Enhanced game you could cause more problems)