Follow the directions in the manual: http://www.mahaenergy.com/content/manual_mhc9000.pdf
More info in the FAQ: http://www.mahaenergy.com/FAQ-C9000/
1. You should reduce the charging current to avoid the temperature rise. That is better than extra cooling. But stay within the recommended currents 0.33C - 1C. However the charger will detect dangerous temperature rise and temporarily halt the charging.
2. There is nothing to gain from "lying" about the capacity. Possibly it may even be harmful. I think the capacity is mainly used when running the break in program, and then the cells are gently "overcharged" using a low current. If you have lied that may lead to more than a "gentle" overcharge.
3. Just top the cells up now and then. If it is LSD/Eneloop perhaps every 6-12 months year or so. Ordinary NiMH perhaps every 1-2 months. No need to do a full charge/discharge/charge cycle often if you don't intend to use the cells, that will only cause extra wear. However if you intend to use the cells after extended storage they will get significantly higher capacity if you give them one or two refresh cycles first. Perhaps 10% or more.
The life of the NiMH cells is reduced by the number of charged/discharge cycles, overheating and chemical change under storage. NiMH cells age the slowest if you store them fully charged.
In the manual it is recommended to refresh the cells every 10 cycles and break in every 30 cycles. But that depends on how fast you rotate your cells. I refresh all my cells once a year, and only break in new cells. And I rotate my NiMH cells so they get used at least once every year.
Try to spread the wear evenly over all your LSD/Eneloop NiMH cells so they all get used at least once or twice every year, that way they are refreshed in use. Try to store them topped up. Discard cells if they don't regain usable capacity after say 3-4 refresh cycles.
For Li-ion it is better to put the wear on as few cells as possible, just rotatat the cells needed for the flashlights that are in use. Store unused spare cells cool and dry and partially discharged. At 3.6-3-7 volts. When one individual cell is too degraded to be usable, discard it and put another in circulation instead.
Li-ion cells age faster if you store them topped up or discharged, and slowest if you store them partially discharged at 3.6-3.7 volts.