@Vincent:
The normal PSU connector and its connected pcb-traces are made to handle substantially more current than the floppy one. The PSU connector and its connected pcb-traces are guaranteed to handle atleast as much juice as the original PSU can supply which is 3A@5V, 0.5A@12V, while the floppy connector plus traces is only supposed to handle as much as a floppy drive needs which is no more than about 300mA@5V, 200mA@12V.. needless to say it obviously can handle more, but you are probably pushing it when powering the whole shebang through it.
If you are using one single powersupply, there should be no problems to power the computer through both the PSU and floppy connector. After all, they are connected to eachother.
/Patrik