Thanks MCT_MR2, I will talk to PAR engineering.  I believe this is the solution I was hoping for!
 
Like anyone I don't want to spend a lot of $$$, but considering how tidy this F20C conversion is I believe it would be a huge injustice to NOT do it properly. 
 
I don't think there will be any change out of $3000 but would consider it money well spent.

Hey Guys, I'm back again having done a fair bit more research.
 
PAR Engineering can indeed fabricate the gearing I need (any ratio I want) but at a cost of $1980.
 
My research has indicated that the "E" series boxes seem to be compatible with the "S" series boxes, and I have found some mention on US sites where they reference the use of the final gearing from the E250F box (4.933) but can't seem to confirm it's compatibility with the S54?
 
Does anyone have any insight or can point me in the right direction?
 
Thanks.

An engine that accepts an s54 box will generally be compatible with an e153. In that sense they are compatible

If you are asking if the e series final drive will fit in an s54, I highly doubt it. The e series boxes are substantially bigger than the s series.

I'm finding a lot of chatter on Celica and Rav4 forums both in the US and UK and swapping "E" series diffs into the S54 seems to be fairly common, I can find plenty of references of the E250F option but can't find anything substantial.
 
If I can't find someone who can say a definite yes or no then I will buy one of each and have a play, though this is not the most ideal scenario.  (still better than forking out almost $2000 just for the gears, which will be a last resort)
 

TBH, there is no cheap option for what you are chasing.

While it's still not a simple solution, I would look at the EA60, EB60 or EB62 Toyota 6 Speed gearboxes.
https://en.wikipedia.org/wiki/Toyota_E_transmission#EB60
They have a combination of crazy 1st gears and diff ratios that should allow you to get up on Vtek and stay there.

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.

Instead of VAFC, maybe consider Hondata which will give you full access to the motor for tuning. Just shifting the VTEC point might require other adjustments to the tune to get the best results from those changes, which you will not be able to do with a VAFC.

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.  :)
 
 

Rav 4 uses a "Narrow" box with some fairly low ratios.
It would likely stand up to the torque of the na Honda.
Identifiable by a pressed steel end cap.
It will be about the same length as the S54.

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.