Hi Lee,
Nice build and nice color--what paint did you use? I like what you did with the exhaust wrap.
If I remember correctly, you won't find many pics of this M113 because it is a test version.
I think it should be pretty safe to base my answers to you on a Zelda "Kasman Armor", since it incorporates the same or similar doghouse and side armor.
Only found one pic of that ammo box you refer to in use, however all other photos show the type which is parallel to the 7.62 machine gun as you can see on my Kasman's link. I guess it's because a parallel ammo box doesn't get obstructed by the shields. But I think you can leave your ammo boxes on since your Zelda is a test version.
Can't commend on the tail lights' guards though, since the only photos I recall seeing of your Zelda(but can't find now) have External Fuel tanks there-with the lights mounted on them.
http://www.angrydogproductions.com/Kasman%20Complete.jpg If you need more information, take your questions to the dedicated idf modelling site.
Nick