Can a patent have more than one multiple preferred embodiments? Where is this discussed in MPEP?
A patent can, and should, describe several embodiments. The preferred embodiment must be described, but it is not necessary, or even desirable, to state which embodiment is preferred. You must not try to hide a preferred embodiment by obscuring it with excessive numbers of other embodiments. Multiple embodiments are helpful for supporting broad claims to whatever elements are common to all the embodiments.
Yes, multiple preferred embodiments are allowed.
608.01(a) Arrangement of Application [R-11.2013]
¶ 6.02 Content of Specification
(j) DETAILED DESCRIPTION OF THE INVENTION: See MPEP § 608.01(g). A description of the preferred embodiment(s) of the invention as required in 37 CFR 1.71. The description should be as short and specific as is necessary to describe the invention adequately and accurately. Where elements or groups of elements, compounds, and processes, which are conventional and generally widely known in the field of the invention described, and their exact nature or type is not necessary for an understanding and use of the invention by a person skilled in the art, they should not be described in detail. However, where particularly complicated subject matter is involved or where the elements, compounds, or processes may not be commonly or widely known in the field, the specification should refer to another patent or readily available publication which adequately describes the subject matter.
I would strongly recommend against describing "multiple preferred embodiments" in a patent specification.
By having a single preferred embodiment, you can easily fight some instances of unfavorable claim constructions using the case law principle that "a claim construction excluding the preferred embodiment is rarely, if ever, correct" (for a more thorough explanation, see http://www.finnegan.com/files/upload/Newsletters/Full_Disclosure/2013/March/FullDisclosure_Mar13_1.html).
If you have multiple preferred embodiments, you would naturally have a harder time swaying claim construction using this principle, though it might not be impossible.
I find it hard to imagine a situation in which having multiple preferred embodiments is better than both the more conventional options of (A) picking one as preferred and describing the rest in the alternative or (B) filing separate applications for each embodiment. Choosing between (A) and (B) is admittedly not easy, and would depend a lot on facts we haven't been given.