Both of those apps predate iOS 4.2. It's possible they never updated the apps for background downloads. You would have to check the version, revision info on their site or the App Store.
Even if they do have it, downloads have a limited time to complete in the background before iOS stops them. With that much to download you may be exceeding that limit. Annoying, I know. But the alternative is the forever downloading app in the background killing your 3G data and battery when you don't know it.
Tough call, especially for those of us with 3G iPads and plans.
Anyway, this is what I would do.
Make sure you've got some time you're willing to set the iPad asside, an hour should be more than enough. Plug it into the charger. Go into Settings >> General and turn Auto-Lock to never. Now start the app and tap on the comic books. I believe that will restart any downloads that have paused (but not 100% sure).
Now wait a frustratingly long time.
Don't forget to reset Auto-Lock when you are done.
Hope that works for you.