What is the best way to lower a limited 1in. I didn't know if a shorter shock or is there a better way. Thanks Dan

 

There are a ton of ways.....

Ohlins or another shock set Progressive 944's 12" but 3 inches of stroke
lowering blocks
Air shocks
12" shocks from a Street Glide or Limited Low

That is a start...
Research on the forums, there are more threads than you can read in a sitting......

All it takes is a wrench and money

 

WHY?
Help us help you. We need information. There are different ways to do things that depend on WHY you want to do it.

 

If you ride 2 up forget the street glide 12 inch shocks. They are terrible even light.....

 

I'm just a little short to be flat footed when stopped. I was hoping by lowering the rear it would make it where I could stop more comfortable.

 

12" shocks are what you want. The limited low would have been the better option as it comes with 12" rear shocks and 1" shorter fork springs.

 

Have Your seat modified then You won't hang up on speed bumps or damage Your pipes backing to curbs.

 

If you are otherwise happy with your shock's performance then avoid changing them out. You could be starting a long, very expensive and time consuming journey trying to achieve a good ride with a lower shock and still end up sorry.
As suggested, consider having your seat modified by Mean City Cycles (do a search and you will find very good reviews, reasonable cost and excellent results), and consider a boot with a thicker sole including have another layer of sole added to existing boots which might just be enough. If you go the seat mod route, an HD parts department should be able to give you a box to ship it. You might be able use the dealer's demo seat for a week while yours is modified. MCC uses an appointment system that works really well, at least that has been my experience in the past.
Good luck!

 

How good are the lowering blocks' and I'll check on the seat. Thanks

 

I'd look at a different seat...I like the ground clearance, etc.
But you've got several good options here.