It is now possible (with the latest version of 3dDeconvolve) to analyze variable duration non-TR-locked events directly. The format of the timing file is a little different than you hypothecate, though.

The option to use is

-stim_times_AM1 k tfile dbBLOCK

where k = which stimulus index this is (1, 2, ...)
where tfile = timing file (format below)
where 'dmBLOCK' means to use the duration modulated 'block' function (for short durations, this is OK for 'events').

The timing format for dmBLOCK input is of the form

30:5 40:7 57.3:9.2
14:2.7 39:12

where each pair is 'start time' : 'duration' (in sec).

Each line of input refers to a separate imaging run, as specified in the -concat command line option.

For more information, see the output of 3dDeconvolve -help, and these documents (which are referred to in the -help output):

[afni.nimh.nih.gov]
[afni.nimh.nih.gov]

Note that you must be sure that you have the latest AFNI upgrades, as the duration modulation is relatively new (was add in early Dec 2008).