After you file

Are you sure it's the IRS and not a state.  Some states do impose an income tax on the net income of form XX-1065

what is the notice number? what does it say? 

a partnership/LLC  is not subject to Federal income taxes but may be liable for payroll, excise taxes and also 

Line 23. Interest due under the look-back method for completed long-term con-tracts. For partnerships that aren't closely held (a H&W LLC is closely held), attach Form 8697 and a check or money order for the full amount, made payable to "United States Treasury." Write the partnership's employer identification number (EIN), daytime phone number, and "Form 8697 Interest'' on the check or money order.
Line 24. Interest due under the look-back method for property depreciated under the income forecast method. For partnerships that aren’t closely held, attach Form 8866 and a check or money order for the full amount, made payable to “United States Treasury.” Write the partnership’s employer identification number (EIN), daytime phone number, and “Form 8866 Interest” on the check or money order.
Line 25. BBA AAR imputed underpayment (Not at all likely). Use this line if the partnership is filing an AAR electronically and chooses to pay the imputed underpayment. For instructions on how to figure the imputed underpayment, see the Instructions for Form 8082. Write the name of the partnership, tax identification number, tax year, "Form 1065," and "BBA AAR Imputed Underpayment" on the payment. Checks must be payable to “United States Treasury” and mailed to Ogden Service Center, Ogden, UT 84201-0011. Payments can be made by check or electronically. If making an electronic payment, choose the payment description “BBA AAR Imputed Underpayment” from the list of payment types.

Line 26 what other taxes could be is a mystery

 

if it is the IRS are you sure it's not taxes you owe on your 1040 for misreporting something on the LLC k-1's

 

I don't think a transcript or copy is going to do you any good but here are the links

you might be better off calling the number on the notice. 

the IRS does not provide an online transcript for form 1065.

there is form 4506 which is for a copy of the return $43

https://www.irs.gov/pub/irs-pdf/f4506.pdf 

there is form 4506-T which is for a transcript of the return - free.

https://www.irs.gov/pub/irs-pdf/f4506t.pdf