<PAGE>

                                                                 Exhibit 10.11.3

                  SECOND AMENDMENT TO STOCK RIGHTS AGREEMENT


          This is the Second Amendment to Stock Rights Agreement (the
"Amendment"), dated September 30, 1998, between RICHARD E. OTTALAGANA
("Shareholder"), PAETEC CORP., a Delaware corporation with its principal place
of business at 290 Woodcliff Drive, Fairport, New York 14450 (the "Company"),
PAETEC COMMUNICATIONS, INC., a Delaware corporation and wholly-owned subsidiary
of the Company with its principal place of business at 290 Woodcliff Drive,
Fairport, New York 14450 ("Subsidiary"), and ARUNAS A. CHESONIS ("Founder").

                                   RECITALS

          A.  Shareholder holds 250,000 shares of Class A common stock of the
Company, subject to certain restrictions contained in a Stock Rights Agreement,
dated July 17, 1998, among the parties (the "Agreement").  Shareholder also
holds 30,000 shares of Class B common stock of the Company, subject to certain
restrictions contained in the Agreement and in the First Amendment to Stock
Rights Agreement dated August 13, 1998 (the "First Amendment").

          B.  The Company has now offered to issue to Shareholder 30,000
additional shares of Class A common stock at a purchase price of $2.50 per
share, subject to certain restrictions.

          C.  The Company, Subsidiary, Shareholder, and Founder enter into this
Amendment for the purpose of confirming Shareholder's additional equity interest
in the Class A common stock of the Company and outlining the rights of
Shareholder and the restrictions imposed by the Company with respect to the
additional Class A common stock to be held by Shareholder.

                                     TERMS

          NOW, THEREFORE, in consideration of the following mutual promises, the
parties agree as follows:

          1.  Issuance of Shares.  The Company confirms its offer to issue
              ------------------
30,000 shares of Class A common stock (the "Additional Class A Shares") to
Shareholder at a price of $2.50 per share, payable in full upon issuance of the
Additional Class A Shares.  A stock certificate evidencing the Additional Class
A Shares shall be issued in the name of Shareholder upon receipt of this
executed Amendment and payment in full of the purchase price.

          2.  Incorporation of Agreement and First Amendment by Reference.  All
              -----------------------------------------------------------
of the provisions of the Agreement shall apply to the Additional Class A Shares
issued to
<PAGE>

Shareholder pursuant to this Amendment, except to the extent that a
provision of this Amendment expressly supersedes any provision of the Agreement
or First Amendment.  Sections 3 and 5 of the First Amendment, which modify
Sections 4 and 2, respectively, of the Agreement, shall also apply to the
Additional Class A Shares.

          3.  Legends.  Each certificate for Additional Class A Shares owned by
              -------
Shareholder shall bear the following legends:

              (a) The shares represented by this certificate were issued to
          the shareholder with restrictions. Neither the shares, nor any
          interest in them, may be sold, transferred, assigned, pledged,
          hypothecated, or otherwise disposed of, unless that transfer is
          expressly permitted by a stock rights agreement, including any
          amendment thereto, between the shareholder and the Company, a
          copy of which is on file at the office of the Company in
          Fairport, New York.

               (b) The shares represented by this certificate have not been
          registered under the Securities Act of 1933, as amended, and may
          not be transferred in the absence of such registration unless the
          Company receives an opinion of counsel reasonably acceptable to
          it stating the such sale or transfer is exempt from registration.

With respect to Additional Class A Shares that are subject to the Company's
Purchase Option, described in Section 3 of the Agreement, however, Shareholder
shall be entitled to a certificate without the legend set forth in subparagraph
(a), evidencing any Additional Class A Shares as to which the Purchase Option
has expired.

          The parties' assent to the terms of this Amendment is confirmed by
their signatures below.

                                    PAETEC CORP.



                                    By: /s/ Arunas A. Chesonis
                                        --------------------------------
                                         Title: President

                                       2
<PAGE>

                                    PAETEC COMMUNICATIONS, INC.



                                    By:  /s/ Arunas A. Chesonis
                                        --------------------------------
                                         Title: President



Address:                             /s/ Richard E. Ottalagana
                                    ------------------------------------
                                         Richard E. Ottalagana
965 Strong Road
Victor, New York  14564


Address:                             /s/ Arunas A. Chesonis
                                    ------------------------------------
                                         Arunas A. Chesonis
18 Buckthorn Run
Victor, New York  14564

                                       3