This is probably way too late to help but I had the same Idea/problem.
on VS. maps, high, wide cannons are very noticeable so I wanted to make a long rail gun like you suggested, (but for stealth)
I heard from http://minecraft.gamepedia.com/Tutorials/TNT_cannons
- that, since tnt is less effective further from the shot, bringing/condensing the charge closer to the shot can increase the effectiveness of the cannon.
So condensing is possible with tnt also (not just pistons. I think TNT is faster, easier to use) ...Its like a cannon that fires charge into the final cannon, you with me?
moving charge closer to the final shot.
so I rail the charge together, instead of the shot, I think this is better as it can happen in the charge's 5 second fuse and so it doesn't need to go very fast, so it can be easier to time)
I did this, and added many stages, ...its slow, but it doesn't matter, as long as it finally pushes charge behind the final shot.
so I was able to move VERY long lines of final charge RIGHT behind the shot, making for one hell of a shot!
my cannon stood about 8m high(?)and 8m wide, and about 30m(?) long. just because I didn't want to make it super long, its a bit wide, tall.
I put the shot 1 block off the ground. And I've ranked my rail gun up to skeptical distances of 2000m - 2600m (It could be west facing)
It gets about 150-300 TNT firing right behind the shot
it leaves the gun at about 15 degrees
I haven't tried these inverter types, I've just used repeaters, and use dispensers all the time now)
(what would happen if I elevated the gun off the ground a bit!?!)
I can give photos of the cannon, since I don't know how to do videos, but let me post that latter.
Since I like to think of stealth, a cannon firing straight can be found by an enemy by following along the one axis the shot came from, right? or you can be retaliated upon.
but would a sideways firing cannon be better?
this is actually what the first cannon here seemed to do, I'm Impressed :3
I've been putting 2 of my guns facing 90 degrees to the same shot to do sideways shots, (I'm currently experiencing disploding cannons, hmm?)
sorry for my long comment, but I do love having a forum about these cannons! <3