I am rather surprised at what you found in terms of problems. Never had those happen to me. The units disappearing could be a graphics glitch with the normal game (you sometimes get ghost units popping up that are unrendered and then disappear again), unit moving too quickly is more likely an issue either with you accelerating the battle time (in which case all units zip around) or playing on a map where there is a paved road over otherwise very difficult terrain (roads make units move faster in battle while difficult terrain makes them move slower). Regarding Lancer disappearing, that is normal mechanics: They only appear at random or when the unit is charging. Otherwise they normally default to secondary weapons.

Strat map:
Are you sure you actually added them to the queue? Sometimes I think I did and then when allocating funds cancel some buildings to build some more elsewhere.

Regarding mods:
CNP should be fine then. I assume its a few name files and possibly a change to descr_strat and campaign_script. The latter two you will have to merge (use a program such as Compare It! and move over name sections only)

Animations likely won't be a good idea to use unless you want all 2H units to act like JHI (very powerful animation, would require significant stat decrease which may mess up autoresolve some more)


Thanks!