Tell ya what bro, I really need that eye doctor appt Wed... I can't hardly see what you got happening there..lol.. What type of air filter you have in there, hopefully a K&N stock replacement. As for water getting in, I can't comment cus I just cant see the first pic. I would say i don't think its going to but... your not going to let too much air in, your most likely still restricted in the airbox anyway.
On a side note, since you spent the money on the new exhaust you really should finish it out with a S&S or a K&N. I can't tell you how much an improvement you will see/feel and you will be so glad you did. I modded my stock air box and it made a nice improvement but once I replaced it WOW! It might seem like a little much to spend all at once but I would strongly suggest doing it when you can afford it.
Last note, if you could update your signature with bike year, model and accy installed it would really help especially when posting in performance section. This way someone knows what you got and may be able to help more...
Safe riddin, hope this helps..
2011 White Vision - Nuvi 550, Lowers, Lloydz 2nd filter, Vic perf filter, CB/Icom, 96 Brake LED's, Clear Signal lens/Switchbacks, VIC Hwy Pegs, Stebel Horn, 7Jurock 15" Shield, PCV, Lloyd ATS and Variable intake, Ness honkers
2004 V92 TC - S1 flash, level 1 slip-on, Ness big sucker K&N, ISO Grips, 4x1.5 Highway Hawg Risers, extra chrome (never too much), JM 2k CB 4' antena, Mustang seat, HD Front TS & Lowers, OD Pulley
Retired Navy SCPO