Just like the title says can i get the road tax done at the small shops or do i need to go to the land transportation office to get it done.

Some will do it for you, some won't - if it doesn't need testing (5 years if I recall correctly) most will.

Found a small shop that i normally use for my scooter to take care of it saves me a trip.

Road tax is same process for any bikes so actually it doesn't matter if scooter or big bike

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They usually do.

I forget the commision they take. Doubt it was more than 100b.

I was late paying my tax one time as I was outside Thailand. The government fine was massive. 4 baht. One baht for each month.