12 week and 16 week old kitten and health concern

Hi all - sorry for the long post but I'm desperate for some insight or advice

I have taken on a feral kitten who was (according to vets) 8 weeks when we first found him living in the abandoned garden next door. He's become very friendly since the first few days of cutely hissing in the corner of his crate.

The problem? - He has terrible runs and has never been able to do any solids, even now! They're (sorry!) a bit noisy and unusually smelly. I've had kittens so know there's something amiss.

Vet checked and is undergoing vaccinations, is FiV/FeLV free. Weighs 1.5 lbs.  Vet just informed us he no longer has Giardia after 2 rounds of Panacur. He also had Coccidia which only showed up after a second test but appears to have been treated with Albon.

My other kitten (pictured on left below) is now 16 weeks old but pesters little one when we try to let them play together. I have a crate and a fold-out pen which was used during little one's treatment.  I have no experience in 2 unrelated kittens and my oldest (tabby) Mieko plays hard sometimes and is a big bully. Mithra the youngest is only playful toward him only when he is safely enclosed otherwise corners up and is afraid but Mieko still swipes at him!

My 2 issues are as follows:

1. Today Mithra had some blood in his runny stool for the first time. I am going to send it off for analysis but as the last test came back Giardia free I don't know that it will help.  The vets I am stuck with are more interested in talking about vaccinations than addressing his diarrhea. :{   It seems that he is also a bit sore down there as if I try to help him after going to the loo he yelps in pain but as he's long fur it's sort of necessary.

- Also my older kitten has been having similar runs and (again sorry for being graphic) noisy poops in the last week or so. I'm worried whatever this is has somehow crossed to him - despite isolating the little one in a playpen since we've had him.

2.  Is there a way to let these 2 sort out some kind of pecking order while Mithra is so small and not yet completely better?  Or do I wait until they are both bigger?  I do not want to make it worse by completely separating them.

Ask the vet to check for tritrichomona foetus. http://www.highgait.com/page/page/3485008.htm

I would continue to wait until the little one's health issues are mostly cleared up before introducing.  You can do all the pre-introduction stuff, exchanging scents, etc as outlined in the behavior forum, but until you know what's causing the diarrhea, I'd wait to fulling introduce them as you don't want them sharing litter boxes just yet.  What are you feeding?  That might be contributing to the problem as well.

This is true. I may have to put him back in his quarantine pen as clearly something is not right still.

I'll ask about that Tritrichomonas Foetus. It sounds awful. Can it be treated? :{  Breaks my heart if bringing in the feral kitten somehow infected our oldest.

Mieko the oldest has been on Petit Cuisine since he was 5 weeks old - "Assorted Seafood  Pack" (http://www.petco.com/product/106956/Petite-Cuisine-Gourmet-Canned-Cat-Food.aspx?CoreCat=OnSiteSearch)

Sometimes Halo - Spot's Stew chicken or Merrick. Anything non-grain or wheat or by-product.  Some dry food such as Solid Gold, Merrick or Wellness.

I have considered changing food brands as the Petit Cuisine is very brothy and looks like tuna but I must say Mieko has grown beautifully and his coat is soft. He used to get occasional bouts of diarrhea though so this isn't technically new. He had it about a month back too.

The little one however is still really small for his age.