Given you're looking at getting a standalone ECU in a few years it's hard to see the value in getting a Chiptorque re-chip (it's not actually a reflash AFAIK) done.
I've been going through this thought process myself since getting my SE and this is the conclusion I've come to.
My understanding is the Chiptorque option is around the ~$1400 mark and unless you take your car up to Qld it's a 'best guess' tune based what mods you've done and as we know, even with the same mods, every car is different. It'll be close but still not as good as it could be.......
Furthermore, if you make any changes to your car you've got to do it all (and spend your money) again!
Now for only slightly more ($1499) you get the plug and play Adaptronic ECU.
http://www.adaptronic.com.au/product/esel039/The main adavantage is that the Adaptronic can be 'adjusted' for any further changes you make over time (you can spread out the upgrade process and spending) and you only have to buy it once rather than get the Chiptorque done then spend almost the same money again in a few years.
The main disadvantage is you need to spend some time getting the base tune stable before getting the full dyno tune done for additional cost. (Say ~$500-1000 for a good one).
As for injectors, the factory ones are just too small for any level of mods and need to be replaced.
I've come to the conclusion that spending extra for good ones that work well at both low level and high level mods/tunes is the way to go (spend once, spend well). The Injector Dynamics ID750 seem to be the sweet spot at the moment and are good for anything upto a silly E85 monster.....
In terms of drivability, the top spec standalone ECUs like the Adaptronic are sophisticated enough that they will perform as well as the factory ECU (in this regard) if tuned correctly by a competent tuner who is given the time to do things properly. PM Apu for his experience in this area.

It may be more painful (costly) to do it upfront but you'll (I believe) get a better result and avoid spending money twice which is better in the long run!
Crapweasel had a Chiptorque previously in his SE which he replaced with the Adaptronic standalone. If I recall correctly from my conversations with him there were no other changes made and he thought the Standalone ECU performed better.... PM him to confirm.
Finally Mania provide a drive-in / drive out service with their Stage 2 kit which has everything you need (given you have already effectively done stage 1 yourself once the intake is installed).
-Adaptronic Select ECU
-Larger Injectors
-Dyno Tuning
-Boost Control Solenoid
- Wideband MTXL (AFR Gauge)
-Max Power Run http://www.mx5mania.com.au/product1538.htm@ $2899 fitted that's pretty close to what you would be looking at by sourcing and fitting your own parts then finding a tuner yourself.
Sorry for the long winded reply but I've been thinking this through myself for many months now and thought you might appreciate my perspective.
