Hi Bob,
Thanks for the suggestion. Right now I'm going to try Tamiya's two part epoxy putty. I dabbled with Squadron's Green Putty for a couple of holes but haven't attempted to redrill the porthole yet. I have a sinking suspicion the green putty plug will just pop out as I drill.
A note on progress. No pictures yet as I'm just filling portholes and sitting trimming and sanding parts in the evenings while my spouse watches TV. I've been told she's getting tired of seeing the back of my head while working at my desk.  
 
 I found an excellent close up picture of one of the aft 5.25" gun turrents so I've decided to try and add a little more extra detail to them. One is almost completed and I'll post a picture showing what I have done.
I've also decided to tackle the cable reels again and will use fine copper wire to simulate the lines.
I know the kit is an old mold and Tamiya's quality and fit is usually first rate, but there are numerous ejector pin marks to repair and many are in awkward spots on the main superstructure. Also, is it just me or do others often find Tamiya's choice of sprue attachments points for parts rather poorly chosen?
While prepping the funnel parts the attachment points are right on the middle of the pieces where raised detail is making it difficult to sand. I've sadly sanded some of that detail off. Considering both the top and botton of the funnels have additional parts to fix there, that seems like the logical place to have put the sprue attachments as they'd be eventually covered. On some photos I've noticed the ridge detail on the funnels is quite prevalent so I may sand all the raised detail off and replace with thin copper wire to make them pop.
We have a long weekend here upcoming so I hope to show some progress pics by then, if I can remember how to post pictures! Thanks for all the posts everyone.