with that budget you're lookin at some used parts or make some changes...
a new 4 channel amp, even a low budget one is going to run you $150'ish. plus you wanted a head unit ($100), a 2nd battery ($50-100), perko ($40), and 4 speakers ($100-200)... thats easily upwards of $400 right there.
id suggest finding a used 4 or even 2 channel amp on craigslist, ditching the head unit and going with just a straight headphone to RCA cable and have just your ipod, no radio. radio's are pretty useless on the river unless you want to listen to the 12+ channels of mariachi music that parker has to offer.
a perko can be wired up pretty easily. you're gonna need another set of battery cables, one from the 2nd battery to the perko, and then from the perko to your starter and distribution block for your ign, lights, radio, etc.. be safe, use fuses.

you'll need another battery tray so it doesnt jump around and attack you as well.
as far as speakers, bigger the better in this case. lets face it we're not going for super sound quality, we're going for "i just want to hear it from the beach." you can always tab in some small supports under the deck to fit whatever size speaker you can. if you can fit a 6x9 in there, go for it. id suggest going to a store and listening to what they have. everyones ears are different. keep in mind that they'll need to be turned up pretty high to be able to hear em over the exhaust of a big block or all the way on the beach. they'll be under the deck and in the rear somewhere. lookin at this pic could u cut a hole in those 2 rear panels and put a speaker in each one?

so the list:
2/4 channel amp $100-150
amp power, ground, speaker wire $20-40
perko $40
battery cables $15
battery tray $20
headphone to RCA cable $10
battery $50-100
speakers $100-200.