It's a bit hard to give a definitive answer to your query, as I do not know what your sub rank is; what capbadge you are; what type of engagment you are on; whether you have completed EFP1/2 etc etc.
2 issues immediately spring out, however.
Firstly, initialling an ACR does not mean you agree with the contents, merely that you have acknowledged the contents. There are individuals out there who believe that soldiers can refuse to sign an ACR - not true. However, script amendments to ACRs must be accompanied by the initials of the initiating officer. This doesn't seem to have happened. Also, it is not massively unusual to have Parts 1&2 initiated without the soldier being aware that the ACR exists. Any number of reasons can conspire to produce such a turn of events, usually absence on long courses, or operational deployments. Your unit has a duty to ensure that they adhere to reporting timelines laid down by your MCM Div.
Your CO has stated that you are 'qualified for promotion once qualified' for a reason. If the system isn't aware that you are qualified (as you claim), then the onus is on you to make them aware.
Additionally, it is extremely unlikely that anyone is attempting to 'do the dirty' on you for a past redress action. Such a move would have to be considered extremely unwise. There are far better ways of hamstringing careers that don't leave such an obvious paper trail. Remember, initiating officers are stating their beliefs in ACRs - and as such, they are very hard to argue against. The deliberate stating of falsehoods in an ACR is serious business!
For a full breakdown on CLM, pop along to your local AEC and ask questions - it's what they're there for, after all.
Acting rank can certainly be awarded in the circumstances you describe, but only within rigidly defined guidelines; ie a vacancy must exist; you must be fully qualified within a 6 month window etc.
Sorry for the lack of definite guidance, but without knowing specifics, it's hard to provide more targeted advice!