Okay cool.. so you do not think my specs are too loose for now?
and how many km do you think I can drive before I have to check again

You are loose, but next shim up will be too tight for "forum consensus". The general thought is you run .05-.07 intake and .07-09 exhaust instead of .03-05 suzuki recomends.

http://gstwins.com/gsboard/index.php?topic=62370.0 - GSJack outlines his numbers, but I've seen people arrive on larger than his exhaust for intake and even a step higher for exhaust.
FWIW, yamaha maxim's from the 80's had the same type of motor and even used shims you can put in a GS in a total emergency - in short, the same thing as a GS1000-550 series - just yamahaized which is basically 2X the GS500 motor. The suggest .005-007 intake and .007-.009 exhaust.
A thicker shim swap means you lose .05. So subtract .05 from yours and you get 2 at .05 and 2 and .03 - sadly the wrong ones are .03 (or atleast 1 is) If you wanna really get technical, I'll do the 2 that are .1 and leave the other 2 alone. Or maybe do the intake that's .08 also but dont touch the .08 exhaust. General suggestion was to run exhaust over .05 whether it be GSJack or many others here and I wont disagree.
BTW I had an oil using motor I flogged for 50K miles and I could if I wanted to check the valves every weekend. Which I did. And found, mine wore loose. So if you see that happening, swap all 4 with 1 step thicker in a 1000 miles or what miles you check next.
On a side note, You should hear each valve and determine how it sounds, and see if it changes. Also part of getting to know the bike.

PS: Sorry .07 for 1 exhaust not .08 - dont touch that, the .1 - meeh, its OK. I'd really not touch any, but you can swap the intakes 1 size up if you prefer.

Cool.
Buddha.

I had them increase with time on the only bike I ran for long enough to need several adjustments in its life with me, but you're free to make your observations on your bike.
As they stand now, you may need one of them elusive 253 type shims (which were only used at the factory) to get them right without being too tight. Run it, if it increases, you're good to swap to the next thicker shim. If it decreases, well you run it till it goes out of spec.
Cool.
Buddha.

Loom was out, put it back in and it wouldn't start. I knew the battery would be flat so jumpstarted it.. figured out afterwards that a negative from the starter to the battery was missing.

So, what have I ruined?

I can jump start it but it can't ride for more than 1km. Upon playing with the electrics today, when trying to start I lose all power. No headlights or anything when on. So, is the starter relay the culprit for this? And not running for more than 1km, could that be the starter or have I also burnt the stator?

Yes, the stock air box would be the best option, but it's such a pain to work on carbs with it that I don't want to go that route. 

Anyways decided to take a chance and change my diaphragms and wow, now the bikes feels like a fun thing to drive! Probably had too much faith in the old 40 years old rubber.

Now i'm able to rev to 7-8k in every gear with a 125 main jet and 45 pilot and the plugs are white, telling me it need's a little more fuel. Taking in consideration Buddha's advice, for my model (original main = 117.5) the mains I should run should be more around 137.5 to 142.5. Time to order some jets!

Here's a picture of the bike  I installed some emgo pipes and the pipe inside also got a baffle to quiet the beast down. Sounded so loud before, I thought I was in the Bosozoku gang!

Kepping you guys up to date, thanks for the help!!

Actually If you have a free flowing pipe in addition to those pods, it will likely follow the same formula as a GS. I'd not touch the pilot, and go +8 or 10 (meaning 2.5X10 - 10 sizes, so 125 becomes 150, not 135) on the mains with 1 washer for the needle.

Some of these older bike had such restrictive exhausts because they were built during the oil shock era and that was a way to get them to use less fuel while still be nice running and torquey.

Post a pic of your carbs preferable the float bowl and top parts open, I'll tell you if you can use the GS jetting method.

Cool.
Buddha.