Arduino seems to brick itself after time

The Mega uses ~75mA. Plus display and other components.
A 100ohm resistor would drop soo much that there will be nothing left.

Remove (short) that bloody resisor.

Replace the three 1n (useless/small value) with one 100n ceramic cap.

Add a 100n ceramic cap across the 470uF cap.

The 12volt rail of a motorbike without battery will be very 'dirty'.
That's why I proposed a diode/10ohm/470uF/100n input filter.
The function of the big cap is to bridge between dips (zero volt) of the alternator.
A diode there stops the cap from discharging to the bike during those dips.
Grounding might be very important. Star-ground everything near LM7809 ground.
And run one ground wire to the bike.
Leo..

How many times has the OP been told this? I wonder why he is not paying any attention?

Grumpy_Mike:
Look you are asking for advice and I am giving you the advice from my 50 years in electronics. That filter with those values are shit. Feel free to make a compleats mess of your project.
Did you actually read that last reply where I told you why it would be a very bad circuit?

I read your post, I don't get why there's the hostility as i'm just asking pretty basic questions and then reply with my thought process to what you guys are saying. i'm sorry if it comes off like i'm being a smart ass or offensive that is not my intent.

ill remove the the three caps/resistor, and ill add the a .1uf capacitor between the input/ground and output/ground of the lm7809 as suggested.

again i'm sorry mike if i offended you i didn't mean it.

Nobody said you were offensive. The complaint was that you seem to not be fully processing the replies.

Are you sure about that 50volt/33mF cap.
33mF (33000uF) is the size of a soda can and costs about $50.00
Leo..

Yes, that is there in place of my bikes battery. picture is too big to add but here is a direct link to it.

Yes, that is there in place of my bikes battery.

So a question that was raised in reply #22 is finally answered in reply #45. And you wonder why we find you not engaging in the conversation. We can't help you unless you fully engage.

It also begs the question of if it is part of the bike's circuit what else is connected to it? Why is this not shown in the circuit as it will have a bearing on the matter.

picture is too big to add

Any image editing program can reduce it to a realistic size.

It is shown in the circuit, right above the fuse box and after the regulator rectifier I'll make it bigger so it's able to be seen better. it is connected to the fuse box, which powers the ignition, coils, lights, and the arduino.

The problem is that a box just saying "Fuse panel" is not all that helpful because it doesn't tell you what is contains or indeed that there is other stuff going off this.
You need to decouple your input power circuit with a pi filter of the type shown as the last circuit on this page.
http://www.thebox.myzen.co.uk/Tutorial/De-coupling.html

I'll add fuse values in a text box so you guys know. Should I be adding that filter you mentioned at the input of the Arduino? or the input of the lm7809 little confused at what you mean by input power circuit.

perkinja:
I'll add fuse values in a text box so you guys know. Should I be adding that filter you mentioned at the input of the Arduino? or the input of the lm7809 little confused at what you mean by input power circuit.

At the input of the regulator circuit.

Should I leave in the 10 ohm resistor and 1n4004 diode as well or should I take those out as well?

I added in the filter at the input per mikes site but I left the resistor and diode there, if they need to come out i'll take em out of there. Here is an update on the schematic. Mike on your website you say the value of the inductor is not too critical but to try to have the biggest I can get my hands on, what would be the lowest that I could swing?

Take the resistor out.

There is no lowest value for the inductor. The higher the value the better is the immunity so the lower the value the less is the immunity. It depends on how much interference you have as to what you can get away with.
That is why I said right at the outset this process is tricky.

You also need a big electrolytic cap on the output of the regulator in parallel with the 0.1uF. This has been mentioned many times before.

Alright I think I've added everything you said in the order you have said mike, I'm going to add the schematic one more time so i can get it double checked before i go ahead and solder everything

in.

You still have no current limiting resistors on the turn signal transistors. That can damage the processor outputs.

Sorry I will place them in, any recommendation on what the value of them should be?

what the value of them should be?

1K

Alright, here is what i hope to be everything you guys have told me to do on the final schematic. Added the current limiting resistors for the transistors and got all the required components earlier today and soldered everything in according to the schematic. I bench tested it and everything is working under my power supplies power so i'll go plug everything in tomorrow and post back with the results.