Good to here you have a copy of the bible

A wealth of information in there . It's one of those books once you start reading everything really starts to make sense.
How often have we all started on something, pulled it out of the box ,began to put it together and then pick up the instructions after half way through..
There are a few fundimentals to just keeping everything in balance and once you look at what you really want from the motor you can make the most by complimenting each modification.
Interesting reading on timing in there, I've been supplying a few of the lads here with programable ignitions and dynatec coils .Straight away they notice an overall improvement.
Go for a ride behind a bike with a stock ECU and then stick the prog ignition inplace and listen to the difference straight away just on the default settings.
The stock ECU is programmed to cover all sorts of fuel octane ratings, emission, noise restrictions and laws and with the capability to take your TPS it gives you a constant 3d mapping on that basic map to start. Even your aftermarket ECU's like ones from Over have a basic map that is programmed on their Over race spec including cams, pipes, headwork and carbs ect.
Then you TPS gives you mapping over this one program.
The beauty of the programable igition is you can taylor your own map to the amount of mods to your own motor and where it is tuned to perform,then save this preprogramme as your own personal in amoungst the other number of presets in there.
There is graph mapping to show through the rev range or just utilise the 100rpm incriments within the program to change the timing where you find that dip in HP from your dyno results.
Something the others don't have because your 3d mapping from the TPS in the stock and other units is from the one and only progam set in default.
Also if your FCR's dont have a TPS ,you can just turn that function off through a simple program. Plus as you've been made aware, you can set your own rev limit on the limiter. Excite the dwell on the spark to suit coil needs.
Straaight away following Alex last weekend up the goat track I pointed out to him there where no more big puffs of black smoke coming out of his exhaust when on the throttle. He noticed the colour change in the pipe too.
Just getting the correct fuel / air mix ,and not loosing that density through heat and a correct burn is a fundimental to getting the most out of whatever you do otherwise you start to fight against the laws of nature and it's all about the nature of the beast between your legs..

Maybe I should rephrase that..

Have a read on the section on exhausts too as this is a complimentary to it all on how your pulse scavanges .
You will then apreciate the beautiful nature of an Akrapovic system and the abundance of low/midrange torque with just under 6H/P gains on a stock motor alone around 4500rpm.
Best mod anyone can do to a TRX with a budjet is to just change the stock ECU with a programable unit.
Sounds like it's all making sense to you and your on the right path.. It's great to see your making the effort and taking the time to understand how and why. Rome wasn't built in a day..
Well done for putting the research in to get the result you want
