Purchasing second hand motor vehicle from an unregistered individual

RCM is applicable..

You have to pay GST under RCM and you may take the credit in the subsequent months

I am currently paying in RCM @ 5% for freight bills and claiming ITC for it in the same month. Is it have to be done in the same manner, if yes what will be the %

The recipient can avail of ITC on GST amount paid under RCM on receipt of goods or services, only if such goods or services are used or will be used for business purposes. The recipient cannot use the ITC to pay output GST on goods or services under reverse charge and should be paid in cash only..

There is no such limit..If you have paid GST under RCM , you may claim the full.

To avoid practical issues, claim it in the subsequent month .

Are you getting any warning message ?

Read notification no.07/2019 central tax rate dated 29/3/19.

Warning message is only for ITC not matching with auto populated data, but that will be the same in consequent months, right?

With % I mean what will be the the gst % to be paid on reverse charge basis, like for freight it is 5%