First of WDYT of the names in general, then any combo ideas?
FIRST NAMES
[name]Thaddeus[/name]
[name]Tobias[/name]
Gethsemane
[name]Jacob[/name]
[name]Jericho[/name]
Issachar
MIDDLE NAMES
[name]Shalom[/name]
[name]Jeremiah[/name]
Methuselah
[name]Nicodemus[/name]
[name]Samuel[/name]
[name]Seraphim[/name]
Issachar
[name]Isaac[/name]
[name]Genesis[/name]
Shadrach
[name]Abraham[/name]
[name]Uriah[/name]
[name]Shem[/name]
Lot
[name]Solomon[/name]
[name]Raphael[/name]
I like [name]Thaddeus[/name] and [name]Tobias[/name] the best from your first name list. [name]Jericho[/name] is cool, but it might make a better middle name.
What about [name]Thaddeus[/name] [name]Jericho[/name] or [name]Tobias[/name] [name]Jericho[/name]?
Depending on your last name, I like the following combos:
[name]Thaddeus[/name] [name]Samuel[/name]
[name]Thaddeus[/name] [name]Shem[/name]
[name]Tobias[/name] [name]Abraham[/name]
[name]Tobias[/name] [name]Solomon[/name]
[name]Tobias[/name] is my favourite name from you list followed by [name]Thaddeus[/name] and [name]Jericho[/name]. [name]Jacob[/name] is too popular for my liking but it’s a fine name too. Gethsemane and Issachar are a little over-the-top for my taste. Most of your names are multi-syllables so it’s hard to get the ideal syllable count for flow.
[name]Tobias[/name] [name]Raphael[/name]
[name]Jacob[/name] [name]Seraphim[/name]
[name]Thaddeus[/name] Lot
Issachar Lot
Gethsemane [name]Isaac[/name]
I would not use Lot, since in the Bible Lot is raped by his daughters which would be a pretty gross story for your kid to read. [name]Genesis[/name] is more of a girl’s name for me. I like [name]Thaddeus[/name], [name]Jacob[/name] and [name]Jericho[/name] from your first list and [name]Jeremiah[/name], [name]Samuel[/name], [name]Isaac[/name], [name]Abraham[/name], [name]Shem[/name], and [name]Solomon[/name] from your second.
[name]Thaddeus[/name] [name]Shem[/name]
[name]Thaddeus[/name] [name]Isaac[/name]
[name]Thaddeus[/name] [name]Jeremiah[/name]
[name]Jacob[/name] [name]Isaac[/name]
[name]Jacob[/name] [name]Samuel[/name]
[name]Jacob[/name] [name]Solomon[/name]
[name]Jericho[/name] [name]Isaac[/name]
[name]Jericho[/name] [name]Abraham[/name]
[name]Jericho[/name] [name]Shem[/name]
[name]Jericho[/name] [name]Solomon[/name]
I like these. I wish more families who want to use all-Biblical names would pick some of the more unusual boys’ names, rather than having [name]David[/name], [name]Daniel[/name], [name]Andrew[/name], [name]Matthew[/name]…those are all great names, but common enough that used together they are boring. I really love [name]Tobias[/name], [name]Nicodemus[/name] and Shadrach, and I like most of the rest.
I don’t think Gethsemane is a good idea, though. It has a cool sound, but to nonreligious people it may sound ultra-religious and very strange, to boot; and to religious people (judging by myself), Gethsemane is a sad name, evoking the suffering of [name]Christ[/name] on the way to the cross. If you really, really love it, I’d recommend putting it in the middle. However, I’ve seen your name lists, and actually Gethsemane seems very tame in comparison to some of your choices. 
[name]Seraphim[/name] is also…strange, but in theory it’s no odder than [name]Angel[/name].
[name]Don[/name]'t think I’d use Lot, either. He wasn’t a great enough namesake to put up with the odd word-name connotation Lot would have.
And [name]Jacob[/name], in my opinion, is on the other end of the spectrum. It’s a good, strong name, but it doesn’t have a great meaning, and any name that has been #1 in [name]America[/name] for 13 years is too popular for me. If you did use [name]Jacob[/name], give him a really striking middle. I adore [name]Nicodemus[/name] in the middle name spot.
And Shadrach is one of my very favorite unusual Biblical boy’s names. I’d put it up front, myself. I’d switch out [name]Jacob[/name] for Shadrach on your lists in a second.
A couple other unusual Biblical boy’s names I really like are Jezreel, [name]Jotham[/name] and Othniel. I also know a little boy named [name]Adonijah[/name].
[name]Thaddeus[/name] [name]Shalom[/name]
[name]Thaddeus[/name] Shadrach
[name]Thaddeus[/name] [name]Shem[/name]
[name]Tobias[/name] [name]Abraham[/name]
[name]Tobias[/name] Lot
Gethsemane [name]Samuel[/name] (if you did use it as a fn, I think a familiar, masculine mn would work best.)
[name]Jacob[/name] Methuselah
[name]Jacob[/name] [name]Nicodemus[/name]
[name]Jacob[/name] [name]Raphael[/name]
[name]Jacob[/name] [name]Uriah[/name] (I do like [name]Uriah[/name] in the middle)
[name]Jericho[/name] [name]Samuel[/name]
[name]Jericho[/name] [name]Isaac[/name]
[name]Jericho[/name] Shadrach
[name]Jericho[/name] [name]Shem[/name]
Issachar [name]Shalom[/name]
Issachar [name]Samuel[/name]
Issachar [name]Shem[/name]
Have fun!
[name]Jacob[/name] [name]Abraham[/name]/[name]Jacob[/name] [name]Isaac[/name]
[name]Tobias[/name] [name]Jeremiah[/name]/[name]Tobias[/name] [name]Abraham[/name]/[name]Tobias[/name] [name]Shalom[/name]
[name]Jericho[/name] [name]Shem[/name]/[name]Jericho[/name] [name]Seraphim[/name]