1) Pertaining to customizing error it is related to configuration where you changed PSA groupings some where you have missed validity periods and etc.
2) Where you have maintained Earliest pers rec date, Do not go for that approach where it gives some impact in future pertaining to past date related issues, better you follow method where SAP is documented it maintain a valid record in 0007.
I.e with "0" Indicator 0 or BLANK:
The employee's actual times are not recorded, and his/her time data is not accounted using the time evaluation program it works as you desired.
Wef 01.01.2015 maintain Indicator 1 in 0007:
The employee's actual times are recorded and he/she participates in time evaluation so that system functions smoothly.
3) I hope that groupings and PDC dates(Master data) is clear then no pint of removing clusters as well just play around with the system after maintaining necessary master data for each pernr.
Regards
Venkatesh