If you place the vehicle in service in 2001 - and decided not to deduct actual travel expenses, but to deduct standard mileage instead - that was your choice - and standard mileage covers all actual expenses including depreciation.
So far honestly speaking your depreciation was deducted - not directly but indirectly as part of mileage deductions. You may not start depreciation from scratch.
Also what so-called "caught up" depreciation may be used only in the first year the property put in service. That include Special Depreciation Allowance
and Section 179 Deduction.
So you put vehicle in service in 2001 and claimed standard mileage - that is OK.
In 2002 you decided that you would get better refund if claim an actual travel expenses instead of the standard mileage method - that is also OK.
The part of actual expenses is a depreciation - that was reported on the form 4562.
But you did not put the vehicle in service in 2006 - and may not deduct depreciation as if you just started to use it in business.
If you purchase a new vehicle - you may decide in the first year if it is more beneficial to deduct actual expenses (including depreciation) or to use standard mileage rate.