Congrats on your amp purchase.  Great prices now too now that the new models have been announced.  Definately go with the SVPre first and foremost, it makes the biggest difference.  As far as installation, I know on the sv112 there is a screw that needs to be removed so you can ground the SVPre.  That screw has a red plastic on it that would be obviously removed.  Also there are leads that need to be soldered to points on the board.  They too may be obvious when the solder is removed.  I think any trained tech could probably figure out when somethings been tampered with.  I have had mine installed for more than a year now, no problems, just fantastic tone.  As far as other worthwile mods, you can place a set of external dipswitches for easy access to the SVPre push modes.  I'm sure there are a couple other mods if you search for them.  I think Space has a mod or two up his sleeve.

Swapping tubes will not void the warrantee.  I replaced all the stock ones in mine for favor of JJ tubes, but the difference was not as dramatic as in other "all tube" amps. The hybrid section of this amp takes away some of the tubes character IMO.

I would go for the footswitch so I could access the wah and volume functions on the amp.  Although I use a Bad Monkey overdrive from time to time to tighten things up a tad and get mroe from the SVPre.

Hope this answeres some of your questions.

Cheers.

Congrats

1) They will be able to tell it was tampered with. You either made the the jump, head first or play it safe and wait the warranty out. The SVpre is awesome, especially if you install the switches to access the push modes.

2) Just more homebrewed ones. I put the switches for the SVpre on the front of my HD100 and changed the LED's that light up the logo to green. Do a search for mods on here and the old forum A7whiny did some a whole bunch of them and gave great reviews.

3) You are going to have to experiment with tubes yourself to see. I'm fairly new to tubes too. Rather than stating with the powertubes, which you should take to the shop to get done. Start experimenting  with the preamp tubes. Just pull the old one out and put the new one and that's it, simple. I've ordered some on Ebay to try out. They can and do effect your over all tone. Plus they are fairly cheap. The JJ ECC83's are pretty popular on here, I ordered some. I also ordered a EH 12AX7. If you are going to do the power tubes, my advice would be go all out. Spend some $$$ for some nice ones. When getting them installed, ask the tech about the biasing. L6 reccomends biasing inbetween cold and hot. See about getting it biased more on the hot side. It'll work the tubes more and wear them out quicker, but you should have more of the tube tone in there.

4) This question is more loaded than it appears. You really need something to change you patches on the SV. The Shortboard is fantastic with the SV. However the effects in the SV are very limited. Most of us have decided that outboard pedals are the way to go with the SV. If you can get away with only 4 channels and no effect swithing for the SV, then you'd be better off with the FBV Express. I'd recommend the Shortboard, see what effect in the SV you can live with and what one's you need, on the SV or not and start building from there.

5) no

Good luck