Ok the Classic Marvel GiJoe, is probably my all time favourtie comic, at least from my childhood. Transformers was good but GI Joe was great.

I've read almost every issue, except the last ones and a few others. I've also been buying the collected classic trades from marvel and IDW, I got most of the new ones online.

Now to your questions.

1. As far as I can tell IDW and Marvel issues are near identical, same covers same break up of issues. I'm a little concerned that IDW might be a little inferior as they did not include the map of Cobra Island for the Cobra Island civil war. I'm pretty sure the Marvel ones included some of the extras like that, but i could be wrong. it's no biggie I guess.

2. The Cobra civil war concludes in 77 (technically 76, but the aftermath is in 77). that's the 8th trade.

3. You should read to the very end!

I assume by "Snake Eyes and Ninja Force" you mean the time when the comic was branded as such due to Marvel marketing. That was pretty corny, but that period also has Andrew Wildman helming most of the art which in my mind was probably the finest art in the comics history. Anyway most GI Joe Fans were more pissed of when Megatron showed up than Ninja Force.

As for story quality, what can I say the story quality of GI Joe goes up and down a bit, but overall it's great. there's a brief dip after the end of the cobra Civil War because the comic went bi monthly 2 issues a month, meaning Larry Hama had to write some very "Earthforce" filler style stories that were a little lacking. but then oh my some of my favourite stories that as a latecomer to GI Joe blew the pants of some the GI Joe stories I read in the TF comic. Yes things got a little silly again with things like the Eco Warriors,the DEF, and yes Megatron, however this was brief. As for the Ninja Force they were handled very well even if the toys were G2 colours. One of the Ninja Force story arcs contains a major revelation regarding Storm Shadow and Snake Eyes past, and Slice and Dice are cobra villains as worthy as Tomax, Xamot, Major Blood and any other of the Cobra second stringers.

In my mind here are some good reasons to keep going (minor spoilers though)

* The Snake Eyes Trilolgy, The Baroness shoots Scarlet and Snake Eyes goes postal. Also the follow up in Borovia

* The revenge of Cobra Commander, Cobra Commander buries his enemies alive and hatches one of his most clever plans.

* The war in Benzheen, A middle eastern conflict which makes the Cobra Civil war look like a skirmish, several members of GI Joe are slaughtered in cold blood.

* More revelations about Snake Eyes and Storm Shadows past, these come in an issue around the Ninja Force period.

*Andrew Wildmans art, some of the silliest issues have the best art in the series.

*Larry Hama's dialog, In my mind one of the things that makes the comic for me was Hama's talent for dialog, sure it's corny but it always has anice flow to it, and some of the words Cobra Commander uses would astound english professors. I also like the way he sometimes makes fun of some of the crazier or more scifi toy designs in the comics, a classic example would be when Cobra Commander meets Raptor for the first time and pays out his costume.

Back in the day most of the GI Joe veterans who started on issue one, regarded the issues from 1-35 as classic, as later issues introduced things like Serpentor and the twins which they found too bizzare. I guess it depends when you started, like you I started with the stories in Transformers but then also picked up issues after the Civil War too. My personal favourite span of issues would probably be from issue 90-116.

Last thing to note, any issue of Marvel GI Joe not written by Larry Hama is almost always terrible, there aren't many but there are one or two real shockers (they usually don't sit well with continuity and have crazy one of characters like Crystal ball ugh!).

You might also want to pick up GI Joe Special Missions as well. These are extra GI Joe stories but they often tie in with the main comic, and many were printed in the UK Transformer comic every couple of issues, at their heart most are just war stories but with GI Joe characters (big fan to this day of the issue where they deal with the former Nazi).