I just finished installing my pertronix this weekend. Sounds like you have a good handle on it with all the information here.
1. Like the guys here said, all you need to do is note the current positon of the rotor button. Install the new distributor so that the rotor button falls as close to the position you noted. Now as long as you install the new cap so that it fires the same cylinder as the old one did, you are in business. Hopefully your plug wires are long enough to reach with the new cap position. (our distributors rotate clockwise...both of them)
(you do not need it to be #1 cyl like the directions say)
2. Wiring....This one stalled me for awhile...I hooked up just like I removed them.. no worky!

The reason it didn't work...I only had 9.7 volts coming to the coil...
NEW ELECTRONIC DISTRIBUTORS WILL NOT WORK WITH LESS THAN 12 VOLTS AT THE COIL! The reason I only had 9.7 volts is the ballast resistor was reducing the voltage (didn't think I had a ballast resistor installed because I never could find it before...it was hidden under voltage regulator)....I put two and two together...thanks to Jeff

You must get 12+ volts at the coil and you must bypass the electronic control....
All I did is cut hot wire to ballast resistor and butt spliced in wire directly to coil.(purple wire for port, purple/yellow for stbd)..two cuts, one splice, that bypasses resistor and ecu all at once.... Walla 12.4 volts at coil...hit ignition...bam she fired right up!
3. Set timing at 5 deg btdc, install red limiters (limits advance to 20 deg)and you should be getting about 25 total advance with factory springs.
These videos will help you get your head wrapped around it a little more.
Call me anytime and I will talk you through it while you are at the boat... Check your PM for my phone number...Call me don't be shy. I would love to help, as many of the guys on here have helped me.
http://www.youtube.com/watch?v=5a2X9mSSlQYhttp://www.youtube.com/watch?v=FHX1yXVyIMg&feature=relatedYour boat is a 1981 and you have points...I don't so your wiring may differ...enjoy
1985 Marinette 29 Sedan bridge
Twin 318s, 660 hours
New Edelbrock 1409 carbs (working like a charm)
Original Electronic Ignition, Blaster 2 coils, 90 deg plug wire universal kit cut to fit
Raw water system
Freshwater always
Located Pickwick Lake, TN,MS,AL
RETRO BOATS ARE COOL
If the guys on this forum take their time to help you, have the courtesy to update your thread with the resolution.