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However, I wanted to include the IG because, IMHO, Marines aren't really an army - they are super elite special forces.  They excel in surgical strikes, boarding actions, and other smaller scale, highly decisive action.
While this is true in 40K, during the Great Crusade and the Heresy Legion forces were far larger, and regularly used as conquering armies rather than merely as elite forces. Recent background has most Legions numbering at around 100,000, and the largest Legion, the Ultramarines, apparently had over 250,000 marines. There are numerous examples in the background where Legion forces conquered whole planets single-handed. ÂÂ
As such, I think having 'pure' Marine forces makes far more sense in a Legion list context than it does in a 40K one. Still, if you really want to include Imperial Army forces then fair enough. One thing I would suggest, though, is only have Company level forces available. This forces people to spend substantial amounts of points on them, rather than taking small cheap detatchments to cover the Marine's weaknesses.
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I've only read the first of the HH novels and haven't seen all the artwork, but doesn't the Whirlwind existing pre-heresy conflict with other sources?
Not as far as I know. There are several examples of Legion Whirlwinds in the artwork, and are mentioned as being used at Istvaan in
Fulgrim. I'd definitely include them, and probably an AA variant as well (effectively a Hunter, although sources are contradictory as to whether they are a post-heresy development or not, so possibly change the name).
Incidentally, I recommend reviewing
this thread for an attempt to confirm as much as possible what was and wasn't available during the Pre-heresy period. Should hopefully come in handy.
Other ideas are sticking the Thunderhawk back in the list (as a lighter, cheaper air assault transport it has a different role to the Landing Craft and Stormbird, and they were definitely available to the Legions pre-heresy) and possibly include Marine superheavy tanks in limited numbers (there are a few examples in the
Collected Visions artwork, for example the 'Fellblade', which appears to be a Marine Baneblade). Such an addition also helps to emphasise that Marine forces were expected to operate as large armies rather than simply elite rapid-response forces as they are in 40K.
I hadn't noticed that Storm Shields were only available to ground-pounding assault squads. Given that, I think they are a perfectly fine addition, and at least partially supported by the artwork as well (there are examples of cc-armed Marine infantry carrying shields in
Collected Visions).
I suspect your points costs are going to need a little fiddling as well. While the 'standard' infantry are cheaper than their equivalents in the Codex list, many of the support formations are exactly the same cost, despite not having ATSKNF. While raising the initiative back to 1+ helps address this to an extent, certainly any formations that rely on shooting rather than engagements (e.g. Land Raiders, Predators) will suffer significantly from the loss of ATSKNF and are going to be overpriced. Such formations should probably be closer to the costs in the Black Legion list (same stats, effectively Initiative 1+, no ATSKNF) than in the Codex one.