This is an excellent question and as you have already seen, not any easy one. The fact that Ephesians begins with some very long sentences does not make the task any easier.
There is another issue that further complicate this one, punctuation. Various Greek texts put the punctuation in different places in Eph. 1.
In the UBS4 critical text there is a period after verse 6 (other Greek texts put a semicolon or none at all). Then the first pronoun in verse 7 can only be referring to Christ. With this punctuation grammatically it would then make the pronoun in verse 9 as referring to Christ. Zerwick (578), in his grammatical analysis of the Greek text says "ἐν αὐτῷ i.e. to be realized in Christ."
One of the best tools I have is the Exegetical Summary series that was produced by the SIL translation group out of Dallas. They present various exegetical questions that arise from an examination of the Greek text and then list in summary form the positions of various translations and commentaries. In my LOGOS software they are all cross linked so it is an excellent tool.
Here is what they have for this question (the abbreviations are the translation or commentary series they come from):
which he-purposed in him/himself:
LEXICON—a. aorist mid. indic. of προτίθεμαι, προτίθημι (LN 30.62) (BAGD 2.b. p. 722): ‘to purpose’ [El, LN, Lns, Rob, TH, WBC, We; KJV, NASB, NIV], ‘to determine beforehand’ [NJB, REB], ‘to plan’ [BAGD, NIC], ‘to plan beforehand’ [LN], ‘to intend’ [BAGD, LN], ‘to set forth’ [NRSV], ‘to decide’ [TEV], ‘to set’ [AB; TNT]. This is also translated as a verbal clause: ‘to cherish the purpose for one’s self’ [NTC], ‘to decree a plan’ [NAB].
b. ἐν with dative object (LN 90.6): ‘in’ [El, LN (30.62), Lns, NIC, NTC, Rob, TH, WBC, We; all versions except TEV], ‘by’ [LN], ‘by means of’ [TEV], ‘upon’ [AB].
QUESTION—To whom does αὐτῷ ‘him/himself’ refer and what relationship is indicated by ἐν ‘in’?
This refers to Christ [AB, Can, EBC, IB, LN (30.62), Lns, Lt, NCBC, NIC, NTC, Si-ed, TH, WBC, We; NAB, NIV, NJB, NRSV, REB, TEV] though some translate only ‘him’. It refers to Christ because the middle voice of the verb itself already incorporates the reflexive idea of ‘in/for himself’ [Lns, NTC, We]. Two commentators think that ἐν ‘in’ indicates the means by which God will accomplish his plan [TH; TEV]: which he purposed (to accomplish) by means of Christ. The remainder leave the preposition ambiguous.
The pronoun is taken as equivalent to ἑαυτῷ ‘in himself’ and refers to God [Ba, Cal, Ea, ECWB, EGT, El, Gd, Ho, My]: which he himself purposed. Here, the connection with προέθετο ‘he purposed’ is so immediate that the reflexive form alone seems the only possibility [El]. The text is speaking of the purposes of God, i.e. what was in his mind, and while God is the planner, Christ’s role was to carry it out [Ea, EGT, My]. The repetition of ἐν τῷ Χριστῷ ‘in Christ’ in the next clause forbids the reference to Christ here. To take it as referring to Christ is to introduce tautology into this passage [Ho].
Glenn Graham, An Exegetical Summary of Ephesians, 2nd ed. (Dallas, TX: SIL International, 2008), 38.
If you were to look up all of the references, one common pattern emerges between the two versions. All of the earlier commentaries (early 20th century and earlier) all say the pronoun refers to God. It is the more recent commentaries that say the pronoun is referring to Christ. Included in that list is Bruce, the expositors series (more conservative), and the Word Biblical commentary series (tends to be more liberal in there conclusions). I am more intrigued by the comment at the end by Charles Hodge "To take it as referring to Christ is to introduce tautology into this passage." At first glance I think at I would side with the latter group in spite of the fact that most of them are earlier works.