I'm using the 44-Pin TQFP 18F4458 in a couple boards I'm doing now. It's all the same family. I'm using only the dedicated ICSP pins to do programming with an ICD2 clone. The shared pins are allocated for other stuff. The only issue I had was I originally forgot to set the dedicated ICSP fuse in the MPLAB fuse setup. Assuming that fuse is set in the software config, it acts the same as any other PIC I've ever used with shared ICSP pins. You should be fine.
As a side note about those 8 bit USB PICs, if all you are using the USB for is a virtual serial port, the USB CDC PIC code takes up a HUGE piece of memory. Plus bootloading with USB isn't as straightforward as with the TX/RX lines. I'd say stick with the FTDI solution unless you need bulk transfer or HID or something.