Critique my setup

Guys - just looking to get into the vinyl space.  I've always been into audio (worked a hifi store when I was younger) and love to do everything with music.  With entering the vinyl space, I'm looking forward to the more involving experience and the more analog sound and enjoyment that comes from spinning records.  I'm also using this opportunity to try out tubes - I've always heard about them, always wanted to try them, never actually had the chance.  Where I live now, there are no hi-fi stores within a few hours, so I'm just biting the bullet and buying from online retailers with good return policies.  

I'm curious what you guys think of the following:
VPI Classic Signature (3D tonearm)
Ortofon Black Quintet MC Cartridge
Manley Chinook Tube Phono 
Jolida 3502 Integrated (comes with EL34 - thinking about upgrading right away to KT150's)
Klipsch RF25 Towers 
Deftech Supercube I (will probably try with/without and see what I like)

I was thinking about the Sonus Faber Venere 3's for replacing my Klipsch towers, they seem to me the weak link here in the system.  

I listen to alt rock, indie, some oldies, rock, and not so much the classical or jazz - although if the right stuff finds it's way into my library, I'll probably listen to it.  

So questions:
What do you think of the setup?
Speakers - are they the weak link here?  Recommendations in the < 3500 space if I was going to replace them?  
Tips/Tricks that you might want to provide while I get started on this journey?

Thanks in advance for your thoughts!
Imo tubes provide a great warm sound, usually associated with the midrange. Sometimes the highs feel as though there is a veil drawn over the speakers. When I had the rogue, I loved the miss and highs, but the low end was too flabby for me, the rogue just didn’t control the lows to my liking.
if you notice, there is a trend to use a tube preamp with a big solid state amp, which should give you the best of both worlds. To me and that’s why I switched from tube back to solid state, you can find a good solid state amp that sounds like a good tube amp but controls the low end.
 There is no such thing as too much tubes in your system. Good tube gear does not sound slow and bloated, that is bad gear or speakers that are in incompatible match with the tube gear.   If you have the proper speakers there is no need to compromise with a solid-state amp. A good tube amp will Soundstage better and do 3-D presence better. 
 Based on your list I would look at different speakers, kill the speed controller and potentially look at other amplifiers.   Most importantly when you're looking at speakers get ones with high-efficiency that have a nominal impedance of at least eight homes and a flat impedance curve.  If you get very appropriate speakers you can go with set or OTL both of which sounds better than regular pentode tube amps. 
I love sonus faber speakers but they would be far from my first choice for your musical preference.  Since speakers are the most important element in a system i would go out and listen to a few.  My first choice would be some revel's, I also like proAc speakers a lot, although contentious- I really like the b&w line, as well as the monitor silver.
I have Primaluna Dialogue HP integrated, and just put the Manley Chinook in the mix.  There is definite synergy with this setup.  Something like the PL would be a better choice than your jolida.  

I agree that your speakers are probably not up to the level of the rest of your system, and I don't think the Sonus Faber would be either.  I recently got a pair of Revel F208s in your price range, gently used.  This would be a good option for you to consider... one of many hundreds of options.  :-)