I've noticed that setting LookupList and LookupWebId not always work. Therefor, I have a function that replace XML attributes in field schema. Take a look at the following code:

public static string ReplaceXmlAttributeValue(string xml, string attributeName, string value)
{
    if (string.IsNullOrEmpty(xml))
    {
        throw new ArgumentNullException("xml");
    }
    if (string.IsNullOrEmpty(value))
    {
        throw new ArgumentNullException("value");
    }
    int indexOfAttributeName = xml.IndexOf(attributeName, StringComparison.CurrentCultureIgnoreCase);
    if (indexOfAttributeName == -1)
    {
        xml = xml.Replace("<Field", "<Field " + attributeName + "='" + value + "'");

        return xml;
    }
    int indexOfAttibuteValueBegin = xml.IndexOf('"', indexOfAttributeName);
    int indexOfAttributeValueEnd = xml.IndexOf('"', indexOfAttibuteValueBegin + 1);
    return xml.Substring(0, indexOfAttibuteValueBegin + 1) + value + xml.Substring(indexOfAttributeValueEnd);
}

I use it like this: Get both lists and the lookup field that you want to set up:

var mainList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/MainList"));
var mainListLookupField = (SPFieldLookup)mainList.Fields.GetFieldByInternalName("LookupField");
var lookupList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/LookupList"));

Replace List and WebId attributes in your Lookup Field's schema:

mainListLookupField.SchemaXml = ReplaceXmlAttributeValue(ReplaceXmlAttributeValue(mainListLookupField.SchemaXml, "List", lookupList.ID.ToString()), "WebId", web.ID.ToString());
mainListLookupField.LookupField = "Title";
mainListLookupField.Update();

Hope this helps!

I've noticed that setting LookupList and LookupWebId does not always work. Therefor, I have a function that replaces XML attributes in field's schema. Take a look at the following code:

public static string ReplaceXmlAttributeValue(string xml, string attributeName, string value)
{
    if (string.IsNullOrEmpty(xml))
    {
        throw new ArgumentNullException("xml");
    }
    if (string.IsNullOrEmpty(value))
    {
        throw new ArgumentNullException("value");
    }
    int indexOfAttributeName = xml.IndexOf(attributeName, StringComparison.CurrentCultureIgnoreCase);
    if (indexOfAttributeName == -1)
    {
        xml = xml.Replace("<Field", "<Field " + attributeName + "='" + value + "'");

        return xml;
    }
    int indexOfAttibuteValueBegin = xml.IndexOf('"', indexOfAttributeName);
    int indexOfAttributeValueEnd = xml.IndexOf('"', indexOfAttibuteValueBegin + 1);
    return xml.Substring(0, indexOfAttibuteValueBegin + 1) + value + xml.Substring(indexOfAttributeValueEnd);
}

I use it like this: Get both lists and the lookup field that you want to set up:

var mainList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/MainList"));
var mainListLookupField = (SPFieldLookup)mainList.Fields.GetFieldByInternalName("LookupField");
var lookupList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/LookupList"));

Replace List and WebId attributes in your Lookup Field's schema:

mainListLookupField.SchemaXml = ReplaceXmlAttributeValue(ReplaceXmlAttributeValue(mainListLookupField.SchemaXml, "List", lookupList.ID.ToString()), "WebId", web.ID.ToString());
mainListLookupField.LookupField = "Title";
mainListLookupField.Update();

Hope this helps!

I've noticed that setting LookupList and LookupWebId not always work. Therefor, I have a function that replace XML attributes in field schema. Take a look at the following code:

public static string ReplaceXmlAttributeValue(string xml, string attributeName, string value)
{
    if (string.IsNullOrEmpty(xml))
    {
        throw new ArgumentNullException("xml");
    }
    if (string.IsNullOrEmpty(value))
    {
        throw new ArgumentNullException("value");
    }
    int indexOfAttributeName = xml.IndexOf(attributeName, StringComparison.CurrentCultureIgnoreCase);
    if (indexOfAttributeName == -1)
    {
        xml = xml.Replace("<Field", "<Field " + attributeName + "='" + value + "'");

        return xml;
    }
    int indexOfAttibuteValueBegin = xml.IndexOf('"', indexOfAttributeName);
    int indexOfAttributeValueEnd = xml.IndexOf('"', indexOfAttibuteValueBegin + 1);
    return xml.Substring(0, indexOfAttibuteValueBegin + 1) + value + xml.Substring(indexOfAttributeValueEnd);
}

I use it like this: Get both lists and the lookup field that you want to set up:

var mainList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/MainList"));
var mainListLookupField = (SPFieldLookup)mainList.Fields.GetFieldByInternalName("LookupField");
var lookupList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/LookupList"));

Replace List and WebId attributes in you Lookup Field's schema:

mainListLookupField.SchemaXml = ReplaceXmlAttributeValue(ReplaceXmlAttributeValue(mainListLookupField.SchemaXml, "List", lookupList.ID.ToString()), "WebId", web.ID.ToString());
mainListLookupField.LookupField = "Title";
mainListLookupField.Update();

Hope this helps!

I've noticed that setting LookupList and LookupWebId not always work. Therefor, I have a function that replace XML attributes in field schema. Take a look at the following code:

public static string ReplaceXmlAttributeValue(string xml, string attributeName, string value)
{
    if (string.IsNullOrEmpty(xml))
    {
        throw new ArgumentNullException("xml");
    }
    if (string.IsNullOrEmpty(value))
    {
        throw new ArgumentNullException("value");
    }
    int indexOfAttributeName = xml.IndexOf(attributeName, StringComparison.CurrentCultureIgnoreCase);
    if (indexOfAttributeName == -1)
    {
        xml = xml.Replace("<Field", "<Field " + attributeName + "='" + value + "'");

        return xml;
    }
    int indexOfAttibuteValueBegin = xml.IndexOf('"', indexOfAttributeName);
    int indexOfAttributeValueEnd = xml.IndexOf('"', indexOfAttibuteValueBegin + 1);
    return xml.Substring(0, indexOfAttibuteValueBegin + 1) + value + xml.Substring(indexOfAttributeValueEnd);
}

I use it like this: Get both lists and the lookup field that you want to set up:

var mainList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/MainList"));
var mainListLookupField = (SPFieldLookup)mainList.Fields.GetFieldByInternalName("LookupField");
var lookupList = web.GetList(SPUtility.ConcatUrls(web.ServerRelativeUrl, "Lists/LookupList"));

Replace List and WebId attributes in your Lookup Field's schema:

mainListLookupField.SchemaXml = ReplaceXmlAttributeValue(ReplaceXmlAttributeValue(mainListLookupField.SchemaXml, "List", lookupList.ID.ToString()), "WebId", web.ID.ToString());
mainListLookupField.LookupField = "Title";
mainListLookupField.Update();

Hope this helps!