Agreed, there is no cheap option.  The 6 speed boxes are a good option and well priced 2nd hand too, I just don't think I can spare the time it would take to re-engineer my setup for them.  I would like to persevere with the S54 until I feel my options have been exhausted.
 
Truth is, I'm enjoying the research and the thought that I'm putting into it.  The more research I do, the more people I speak to the more I'm learning and the better informed will be my decisions.  I didn't ONLY buy this car to drive and track but to play with.  I'm pleased with the direction Thomas has taken with this modification (one of the things that appealed to me about this car) and intend to continue.  His reasons for keeping the S54 box are very good, especially for track work.  All other boxes I have looked at have noticeably higher internal drag coefficients based on internal mass, rolling mass and torsion forces.
 
I really don't think I will know EXACTLY what gearing will be needed until I get the Vtec tuning sorted out, I recently bought a VAFC-2 on ebay but looks like it may be a scammer!  :(  After ebay refund my purchase I will buy a VAFC-Neo and put the car on a dyno.

Thanks Knightrous, I had a look at an EB62 today at the wreckers (keeping all options open) and it will actually bolt up to the adaptor plate I already have and the linkages are reversable, but it is longer than the 5 speed boxes and would actually be about 30mm into the cars subframe.
 
I looked at Hondata and it is definately a better unit, has better resolution, data logging and allows the timing to be altered.  In contrast the VAFC2 can't modify the timing, but does allow tuning a fuel offsett at up to 12 points in the rev range and will still function off the factory map (which is actually pretty good) so should adequately be able to compensate for kicking in the Vtec a bit earlier.  I don't want to go hard core track setup, but rather keep a safe tune so I think it might do.  Besides, I got it for $200.....  Its worth a try.  :)
 
 

Hi Falcon, thanks for that.  I'm hoping that it being a narrow box the diff casing will be the same as the S54 and allow for a transfer of gearing, I think I have tracked an E250F box down really cheap so hopefully will have both boxes apart and able to check for certain.
 
Fingers crossed.

Thanks for all of your input everyone, it has been very useful.
 
A few things about me:
 
I have been modifying Japanese sports cars since 2004 and have built an SC22 RX7 Tarmac Rally car which is currently running in the CAMS Improved Production Series in NSW, a S5 FC3S RX7 Turbo that won the South Australian Tarmac Rally a few months ago as well as a 1984 Corolla Gymkhana car which doesn't seem to be able to win anything at all.....
 
So while I'm new to MR2's I'm not new to modifying. I have a very meticulous nature with an engineering background, so appreciate the finer details.  I seek out experts but if I can't find someone who can say "yes I've tried that and it does/doesn't work" then I will experiment.  If I get the diff gear set engineered for my car and it breaks at some point then I need to have a new one made up, if I can find an off the shelf solution and it breaks then I just get another one and put it in.  I enjoy this type of modifying, it's challenging and it excites me almost as much as driving at unsafe speeds around a racetrack.
 
I use professionals to do my work for me so I am not going to be stripping any gearboxes myself anytime soon, besides I like warranties.  :)
 
If you see me at the track I hope you will wander over and say hi, and please be courteous enough not to laugh at my driving (fake it if you have to).

Another option might be to look at the E250F gearing mixed with a Camry E53 gearbox (Came with pre-1994 3VZ Camrys).
 
It will bolt up to the adaptor you have, would require SW20 turbo drive shafts and hubs and would allow you to mix the E250F/E53 gears. I've seen this done with 3VZ Rav4, check it out here:
http://strav3vz.blogspot.com.au/2013/05/e53-to-awd-transmission-conversion.html
http://strav3vz.blogspot.com.au/2013/05/dissasembling-e250f-e53-transaxles-1.html
http://strav3vz.blogspot.com.au/2013/05/dissasembling-e250f-e53-transaxles-2.html
 
I believe if you can source an E53 and use the E250F 1st gear and diff, then use the E53 2/3/4/5 gears, this will give you a tighter box then the E250F. I was intriqued and came up with this table comparing S54, E53, E250F and a E53/E250F hybrid.
 

5th gear would let you cruise at 100kmh @ ~3500rpm, which will let you keep some fuel economy...
 
Infact, out of curiosity, I ran the numbers comparing the three 6 speeds and a hybrid of them and an E53/E250F is closer then those too.

 
Food for thought?

I get your concerns Falcon, which is why I felt to need to share a bit of my history so you guys know I'm not just some hack.  I'm very patient and meticulous and will follow a trail of breadcrumbs as far as it will lead me.  :)
 
Damn Knightrous!  If I don't owe you a carton of beer by the end of all this then there is no justice in the universe!
 
My research has indicated that the E53 and the S53 are the same box with different gearing, the S53 is the predecessor to the S54 and internally are fully compatible.  Does this sound right?  If so then your research would suggest that the E250F final gear set is a direct fitment into the S54?  I know there is no cheap option but I'm also balancing the cost V's delivery, I may have to sacrifice something to safe a few pennies.
 
Will I also need to address the driver side drive shaft clearance issue Thomas was faced with?
 
The E53/E250F hybrid DOES look like it would be an exceptional budget track day box, probably best bang for buck.
 
Also, I found some more interesting reading:
http://www.celicatech.com/forums/archive/index.php/t-54182.html?s=8f38b97d3909796140c2e5274c1010bf
 
There are definitely options out there, I find myself spending a lot of time on the Celica forums...  They do a lot of cool stuff to their cars.

sir_smeghed
My research has indicated that the E53 and the S53 are the same box with different gearing, the S53 is the predecessor to the S54 and internally are fully compatible.  Does this sound right?  If so then your research would suggest that the E250F final gear set is a direct fitment into the S54? 

 
I'm going to say no based on the following:
 
The E-series boxes all share a common diff size that can be swapped. You can take a diff from an E51 AW11 SC gearbox and fit it into an E153 SW20 Turbo gearbox. You can also fit it into an E58 AE101 Corolla gearbox.
 
None of the E series diffs work in an S-series gearbox. The only diff that does fit in an S series is a C-series. It's very common for people to steal a torsen diff from a C56M or C60 gearbox and fit it into an S54.
 
The E-series gearboxes feature an internal oil pump driven from the output shaft. The S-series gearboxes all rely on the diff flicking oil onto a catch tray. And since you require the output shaft to be swapped with a crown wheel for a diff swap (To maintain PCD and bearing spacing like Falcon mentions), you will not get that to work between an E250F and an S54...

If you have a look at my calculations on page 1, you will see the ratios are fairly close to the hybrid box. the K20 is 67kmh in 1st vs 53kmh for the hybrid box


2nd is 103kmh k20 vs 101kmh
3rd is 144kmh k20 vs 155kmh

As for coolers on E series boxes, there is a steel pipe which runs outside the case on the underside which provides some cooling, however you can splice into this and run an external cooler. This is what my used gearbox had when I first bought it