Welcome to the silent service Sailor Steve. A period of time ashore learning the ins and outs of the fleet boat is very normal just hope its only a short time and then you can hunt some maru soon!!
BTW I did exactly the same thing with SH3, bought it before my computer at the time could handle it so I had it there as soon as I upgraded.
PS prepare to have your socks well and truly knocked off when you load up ROW and some of the other goodies on the SH4 mod forum!