Ok, i will try to post my guesses about the issues you posted:
The rifle itself is a child of the Rifle_Springfield node and is therefore affected by the movements of this node, if you move the rifle to another node they mesh of the rifle will also be affected by the this movements and no longer by the movements of the Rifle node.
You could try to work with the Rifle_Springfield bone in the animation to set the position of the rifle in the animation and i wouldn´t rig (or attach) the weapon to any other node. To get this node also imported you have to activate the "import extra skeleton nodes as bones" option. (unforuntally it would be good to remove the weapon effect node, the sounds node, the effects node from the imported mesh). If you have trouble doing this you could attach a second instance of the rifle to the hands and work with manual added visibilites controllers in the kf to "switch" between the weapons and the effect placeholders.
The effect itself is played at the position of the RIFLEBLAST_MODERN placeholder node in the nif, if you use the Rifle_Springfield bone to set the position of the rifle, it should automatically have the correct position (it´s also a child of the Rifle_Springfield bone and therefore also affected by animation attached to this bone). If you choose another way you could add a new node (eg a copy of RIFLEBLAST_MODERN called RIFLEBLAST_MODERN2) and use this node as placeholder node in the kf (editing the text keys of the animations and exchanging the name of the node there)
Also looking at your blend i saw that you didn´t set the framerate to 30 FPS. It´s important for civ4, because some animations have fixed sequence lengths - and differences from this length can cause problems. A second issue could be that your strike animation is to short, strike has a fixed frame length of 21 frames, your animation has only 15 frames atm. [or to be more exact: number in the flowchart +1 and 30 FPS, so you should have 22 frames in the animation, otherwise the length of the exported kf is not identical to a similar vanilla kf] Also if you alter the strike animation you must/should also alter the fortify, fortify idle, hurt and die animation. Because looking at the animation flowcharts all this animations are linked. And i believe that differences between end position in one and start position in another of this linked animation sequences can cause problems.
i attached a not in game tested version of your kf with fixed length (means 22 frames) and informtation for the Rifle_Springfield node to fit to your soldiers position (to work the weapons should be like in the vanilla infantry nif a child of the Rifle_Springfield and not of the hand bone)
and after all this: your work looks really nice so far
edit:
your UI problem could be caused by a missing reference file - i see you renamed the kfm to infantry_america.kfm (i guess it´s a copy from the infantry.kfm), and there is no infantry.nif. If your kfm is an unchanged copy, the kfm refers to a master nif (infantry.nif), if this file isn´t in the same folder the games produces errors (with python errors activated you have a lot to click). I guess this is the reason for the UI problem.
To check this, try to open the kfm with nifskope, if you see a model the reference nif is there, if you see no model, your reference nif is missing. If it´s the second, try to rename one of your nifs to infantry.nif (or copy the vanilla one in the folder or change the name of the reference nif in the kfm)