It's a very, very long time since I was doing any of his stuff at school, and that was plays rather than sonnets, so I'm not sure I can help much.
First the easy bits.
I thought 'thou' and 'thy' are synonyms, so what does "thou hast thy 'Will' " mean? No, they are different forms of speech connected with you and your(s). This comparison might make it more apparent:
I, me, my, mine.
Thou, thee, thy, thine.
An exception is that you will often find thy -> thine before a vowel (like a -> an).
To boot is an expression still used occasionally and roughly = what's more/as well. In this case I think it is being used rather as a comparative with overplus as a superlative. So roughly ' you have X, lots of X, incredible amounts of X'.
Now that brings us to the question of what X (or rather will) is, and this is where I begin to get into dificulty as my education is now long ago!
The sonnet is obviously quite bawdy and relies on puns created by various meanings of the word will.
As I recall will in the days of The Bard could mean Will (name - indeed his own), will (as in future tense), wish, desire, lust, both male/female genitals, copulation. There are doubtless others in there - you may find Googling helps you find them.
Given this it may be impossible to paraphrase the sonnet in one, definitive way. A lot may depend on how the listener perceived the words in that context (or how the speaker intones them). That, like the double-entendre of today, probably depended on how dirty-minded the listener was. In those days probably very!
How correct my last paragraph is I don't know, it may be that Shakespeare had a specific sequence of meanings in mind, for instance the lines "Wilt thou, whose will is large and spacious, Not once vouchsafe to hide my will in thine?" seem fairly obvious, others less so.