Crystals, IBD and already on canned food

Background: So I have a problem fur baby .... through this website I have figured out his lifelong GI issues is more of an IBD issue than allergies like I thought before (can only eat rabbit, pork, and duck - no grains, potatoes, peas, guar gum, carrenaguar, agar etc).  So I finally got him consistently solid on natures variety instinct rabbit and pork canned food with fresh cooked duck, pork, rabbit and quail meat every so often (when I have extra money and time lol).  He then starting getting bad separation anxiety when I moved him into my own house because I would be gone 8-10 hours at a time, stress caused him to have soft stools again - a great probiotic from riva's remedies and slippery elm fixed flare ups.  Enter Yeti and they are best buddies (bouncing off the walls together right now) and the separation anxiety gone - awesome!

A few weeks ago I noticed his pee was really smelly - I don't normal notice a urine smell from the litter I used, thought it was maybe change of formula in the litter that wasn't working as well.  Over this time Yeti started leaving a few kibble in his dish for Boomer to eat .... which of course he is extremely sensitive and huge problems comes from kibble.  Or boomer would find a bit of wet food that wasn't licked clean, etc etc.  However he would get soft stools for a day and he fine - no pooping blood or glops of mucus like he use to. 

Current Problem: However he got a bladder infection a week ago (peed rust coloured in the bathtub), started the usual cranberry extract daily (he use to get bladder infections regularly from the diarrhea - he actually got a bacteria and mucus plug and was blocked).  It seemed to clear up - but happened to pee on a blanket in front of yesterday so I thought I would take the opportunity to test it and ensure the infection was gone because the smell was sooooo strong!! 

Results - negative for bacteria but 4/4 positive for styruvite crystals!!!  He has NEVER had one crystal in any other test and there has been lots over the 8 years I've had him. 

Now obviously the vet wants him on vet food, homecooked or raw (I have an awesome vet).  But everything I have read and looked at he shouldn't have crystals and I'm nervous about the amount in the samples (I got to look and there are A LOT).  He is already on 100% canned or cooked meat, drinks a bowl of water on top of that, should be less stressed from having a friend now (I started him back on rescue remedy just in case) which most people say water is the most important part of urinary health.  He also is peeing normal amounts and not upset in the litter box (which he gets with his typical infections).

The only things I can think of are the following two factors - 1) the urine sample sat in my fridge for 4 hours before I could get it tested.  My research says crystals can occur from the sample sitting.  I think I will get a cystosensis sample done around Christmas and test this theory ......

2) I have extremely hard water here and do use tap water for the kitties - one dish of water will leave a mineral layer on the sides of the dish.  I'm wondering if this is enough calcium and magnesium to cause problems?  I have switched them to brita water.

Any tips or food/medication help would be greatly appreciated (he is not on raw because I have tried for 4 years and he will not eat it).

Wow..it does sound like he SHOULDNT have crystals, based on his diet, but I think some cats are just prone to them, no matter what. 

As to the water, I think switching to a brita filter is a great idea.  We also have extremely hard water, and I'm now on my third kidney cat.  So...nothing but filtered water from here on out for my furkids.  (Plus low carb canned food only with extra water added at every meal, and all treats are freeze dried raw like Stella and Chewy's) 

Maybe you could try plugging in Feliway Diffusers in your place, just in case there is any stress there.  It's supposed to realy work on urinary issues partaicularly.  Plus I LOVE how mellow Rescue Remedy makes them . 

I don't know about the urine sample having been in your fridge...did your check with your Vet on that?

My vet won't test home collected urine samples unless I can get them into their office within 15 min. They told me that any longer than that will throw off the results. 

You say that he had a bladder infection, but then that the urinalysis showed no bacteria? 

Ask about methioform tabs for your kitty. It's a sulfur-based amino acid that acidifies the urine. 

Yup he had his typical bladder infection symptoms (whining and peeing in front of me on blankets and boxes), started his cranberry supplement - 450mg cranberry daily. I also switched him to straight duck meat for two days before I added back in his canned food since there was blood present (urine sample was rust coloured).

So I guess I have proof that the cranberry DOES cure bladder infections

I'm definitely going to get a better sample done before I panic too much ..... Lol. I did find lots of research that said crystals form in urine that sits.