If I use the Dow 795, would bolts every 4" be good?
DC 795 is a pretty good adhesive, so bolts every 4 inches should be fine. (see pic above in previous post)
If you're going to cut the plexi yourself, make a plywood template and use a router for a better edge. It's usually worth while to take a template to a plastics place and have them cut it for you ... the fees are modest and they'll probably do a better job.
I'd avoid the temptation to use flat head countersunk bolts - pan heads will work best. Do overdrill the holes. Do not over tighten to the point of causing localized deflection of the plexi at the bolt location. Let the sealant fill the space. If you're worried about the bolted "look", carefully paint out the boltheads in black afterwards.
Dry-fit your new ports and trace the outline on the cabinside in pencil and at the same time trace the INNER profile on the protective paper on the inside. Remove the ports and carefully cut the line you traced on the inside, and peel off the outer rim of paper/plastic (leave the center portion in place, it will protect the inner window from squeezed out sealant) . Rough sand this outer inside surface to improve the adhesion bond. Mask off the interior cabinside and then go back outside and carefully mask off a line 1/8 inch or so outside the traced line on the cabin.. Paint out the hull surface as zzgata suggests (we did that) or be sure to lay on the (black!)sealant in a continuous solid layer inside the masked off area (which I've done on a subsequent project) this makes sure that you can't 'see' the lighter coloured glass under the installed plexi.
Use plenty of sealant, and simply wipe away what squeezed out onto the masking tape inside and out. Finally, lay a bead of sealant around the edge of the newly installed plexi, and with a soapy gloved finger smooth it out so it covers the joint and the outside edge as well leaving a 'wedge' of sealant that goes to the outside edge. This makes a good "shingle" to shed water from the cabinside out to the outside of the window, discouraging any path between the plexi and cabin.
Once all the excess sealant is cleaned up, the golden moment: peel away the protective paper/plastic and masking tape and admire your smartly trimmed, clean installation!