<PAGE>

                                                                 Exhibit  10.6.4

                   THIRD AMENDMENT TO STOCK RIGHTS AGREEMENT

          THIS THIRD AMENDMENT TO STOCK RIGHTS AGREEMENT (this "Amendment") is
made as of this 4th day of February 2000 by and among Joseph D. Ambersley (the
"Stockholder"), PaeTec Corp., a Delaware corporation (the "Company"), PaeTec
Communications, Inc., a Delaware corporation and wholly-owned subsidiary of the
Company (the "Subsidiary"), and Arunas A. Chesonis ("Mr. Chesonis").

                                   RECITALS
                                   --------

          A.  The Company, the Subsidiary, the Stockholder and Mr. Chesonis are
parties to a Stock Rights Agreement dated as of July 17, 1998 (the "Stock Rights
Agreement") and amended as of August 13, 1998 ("Amendment No. 1") and September
30, 1998 ("Amendment No. 2").

          B.  The Board of Directors of the Company has authorized the issuance
and sale (the "Series A Preferred Stock Placement") of 134,000 shares of a new
series of preferred stock of the Company, designated the Series A Convertible
Preferred Stock, to the purchasers (the "Purchasers") listed on the Schedule of
Purchasers to, and pursuant to the terms and conditions of, an Equity Purchase
Agreement (the "Purchase Agreement").

          C.  As a condition to the consummation of the Series A Preferred Stock
Placement, the Purchasers have required that the Company, the Subsidiary, the
Stockholder and Mr. Chesonis further amend the Stock Rights Agreement (i) to
provide that all Class B Shares (as defined in the Stock Rights Agreement) shall
automatically convert into shares of Class A common stock, par value $0.01 per
share ("Class A Common Stock"), of the Company in specified circumstances and
(ii) to clarify that to the extent that any securities are required to be
excluded from a registration pursuant to the "cut-back" provisions of the
piggyback registration rights granted to the Stockholder pursuant to the Stock
Rights Agreement, the securities to be included in such registration shall be
determined on a pro rata basis among the holders of shares participating in the
                --- ----
offering pursuant to registration rights granted by the Company, based on the
number of shares of common stock requested to be included by each such holder in
such registration.

          D.  The parties to the Stock Rights Agreement desire to amend the
Stock Rights Agreement to induce the Purchasers to consummate of the Series A
Preferred Stock Placement.
<PAGE>

                                   AGREEMENT
                                   ---------

          1.  Defined Terms.  All capitalized terms used in this Amendment
              -------------
without definition shall have the meanings given to such terms in the Stock
Rights Agreement, as amended.

          2.  Automatic Conversion of Class B Shares.  Notwithstanding
              --------------------------------------
anything in the Stock Rights Agreement, Amendment No. 1 or Amendment No. 2 to
the contrary, the parties agree that, as provided in the Company's certificate
of incorporation as amended in connection with the Series A Preferred Stock
Placement, (the "Restated Certificate of Incorporation") each Class B Share
subject to the Stock Rights Agreement (as amended) shall automatically convert
into one share of Class A Common Stock upon the date (the "Termination Date")
that the Stockholder ceases to be employed by the Company or any subsidiary
thereof unless, at the Termination Date, Mr. Chesonis shall (i) be the Chairman
of the Board or Chief Executive Officer of the Company, (ii) be the beneficial
owner of shares of Class B common stock of the Company and (iii) have the power
pursuant to a proxy to vote the Class B Shares on all matters on which such
Class B Shares are entitled to vote, provided Mr. Chesonis personally exercises
such power and does not delegate the exercise thereof to any other person.  If
subsequent to the Termination Date, any condition specified in clause (i), (ii)
or (iii) in the preceding sentence shall cease to be in effect, each Class B
Share shall immediately be converted into one share of Class A Common Stock.
All other terms and conditions of the Stock Rights Agreement, as amended, shall
continue to apply to such shares of Class A Common Stock upon such conversion.
In the event of any conflict between the provisions of this Section 2 and the
provisions of Article V of the Restated Certificate of Incorporation with
respect to such mandatory conversion, which shall include, without limitation,
any additional mandatory conversion events specified in such Article V the
provisions of Article V of the Restated Certificate of Incorporation shall
control.

          3.  Amendment of Section 6(b).  The fourth and fifth sentences of
              -------------------------
Section 6(b) of the Stock Rights Agreement are hereby deleted and replaced and
superseded in their entirety with the following sentence:

     "Notwithstanding any other provision of this Section 6, if the managing
     underwriter advises in writing the Company and the Stockholder that
     marketing factors require a limitation of the number of shares of common
     stock to be underwritten and sold in such offering, the managing
     underwriter may exclude some or all of the shares of common stock to be
     sold in such offering from such registration, and the shares to be included
     in such registration shall be allocated pro rata among the holders of
                                             --- ----
     shares participating in the offering pursuant to registration rights
     granted by the Company (including demand and

                                       2
<PAGE>

     piggyback registration rights), based on the number of shares of common
     stock requested to be included by each holder in such registration."

          4.  Binding Effect.  This Amendment shall be binding upon and inure to
              --------------
the benefit of the parties hereto and their heirs, executors, administrators,
successors and assigns.

          5.  Governing Law.  This Amendment shall be governed by, and construed
              -------------
and enforced in accordance with, the laws of the State of New York, except that
if any provision of this Amendment or any part of any such provision would be
illegal, invalid or enforceable under such laws in connection with a suit or
proceeding validly instituted in another jurisdiction, then the laws of such
other jurisdiction shall govern insofar as is necessary to sustain the legality,
validity or enforceability of such provision or any part of such provision.

          6.  Captions.  Captions to the Sections in this Amendment are for the
              --------
convenience of the parties only and shall not affect the meaning or
interpretation of this Amendment.

          7.  Enforceability and Interpretation.  It is the intention of the
              ---------------------------------
parties to this Amendment that the terms and provisions contained in this
Amendment shall be enforceable to the fullest extent permitted by law.  If any
term or provision of this Amendment or the application thereof to any Person or
circumstance is construed to be illegal, invalid or unenforceable, in whole or
in part, then such term or provision shall be construed in such a manner as to
permit its enforceability under applicable law to the fullest extent permitted
by such law.  In any case, the remaining terms and provisions of this Amendment
or the application thereof to any Person or circumstance, except those terms and
provisions which have been held illegal, invalid or unenforceable, shall remain
in full force and effect.

          8.  Counterparts.  This Amendment may be executed in one or more
              ------------
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

          9.  Additional Documents.  Each party hereto agrees to execute any and
              --------------------
all documents, instruments, certificates and communications deemed to be
necessary or advisable by the Company to effectuate the purposes of this
Amendment.

                           [signature page follows]

                                       3
<PAGE>

          IN WITNESS WHEREOF, the parties hereto have executed and delivered
this Amendment with full force and effect as of the day and year first written
above.

                            PAETEC CORP.


                            By:   /s/ Aruna A. Chesonis
                                 ---------------------------------
                            Its:  CEO, Chairman and President
                                 ---------------------------------


                            PAETEC COMMUNICATIONS, INC.

                            By:   /s/ Aruna A. Chesonis
                                 ---------------------------------
                            Its:  CEO, Chairman and President
                                 ---------------------------------


                               /s/ Aruna A. Chesonis
                            --------------------------------------
                            Arunas A. Chesonis

                               /s/ Joseph D. Ambersley
                            --------------------------------------
                            Joseph D. Ambersley

                                       4